Private Entities (Permittees)

NPDES Permit Writers’ Manual for CAFOs

Contents
1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.1. Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.2. Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.3. Purpose and Organization of this Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
1.4. Limitations of the Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

2. AFOs and CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.1. Animal Feeding Operations (AFOs) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2. Concentrated Animal Feeding Operations (CAFOs). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
2.2.1. Types of Animal Operations Covered by CAFO Regulations. . . . . . . . . . . . . . . . . . . . 2-5
2.2.2. Animal Types Not Listed in CAFO Regulations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
2.2.3. AFOs Defined as Large CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
2.2.4. Practices Constituting Poultry Operation Liquid-Manure Handling . . . . . . . . . . . . 2-7
Wet Lot and Dry Lot Duck Operations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8
2.2.5. AFOs that Are Medium CAFOs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8
2.2.6. Operations under Common Ownership. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.2.7. Operations with Multiple Animal Types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.2.8. AFOs Designated as CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
2.2.9. Process for Designating an AFO as a CAFO. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
2.2.10. EPA Designation in NPDES Authorized States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16

3. Appropriate Permitting Strategies for CAFOs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.1. NPDES CAFO Permit Applications and Notice of Intent. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.1.1. CAFO Permit Application or Notice of Intent Requirements for
Nutrient Management Plans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.2. Individual NPDES Permits for CAFOs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.2.1. Developing Individual NPDES Permits for CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
3.3. NPDES General Permits for CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
3.3.1. Developing NPDES General Permit for CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
3.3.2. Watershed-Based NPDES Permits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9
3.4. Procedures for Permitting Authority Review and Public Participation Before
Permit Coverage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
3.4.1. Individual Permit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
3.4.2. General Permit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10

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4. Elements of an NPDES Permit for a CAFO. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.1. NPDES Effluent Limitations and Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
4.1.1. Overview of Applicable Technology-Based Effluent Limitations and
Standards. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
ELG Animal Sectors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
CAFOs That Are New Sources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
CAFOs That Are New Dischargers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
4.1.2. Technology-Based Requirements for the Production Area of Large CAFOs. . . . . . 4-8
Operations Covered by Subpart A—Horses and Sheep. . . . . . . . . . . . . . . . . . . . . 4-8
Operations Covered by Subpart B—Ducks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
Operations Covered by Subpart C—Dairy Cows and Cattle Other than
Veal Calves and by Subpart D—Swine, Poultry and Veal Calves. . . . . . . . . . . . 4-10
4.1.3. Technology-Based Requirements for the Land Application Area of
Large CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-14
4.1.4. Best Professional Judgment (BPJ) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-17
4.1.5. Industrial Stormwater Discharges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-19
4.1.6. Other Technology-Based Limitations that Apply to Discharges
from CAFOs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20
4.1.7. Nutrient Management Plan (NMP). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-21
Minimum Measures that Must be Terms and Conditions of the
NPDES Permit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-21
Including the Terms of the NMP as NPDES Permit Terms. . . . . . . . . . . . . . . . . 4-22
Establishing the Minimum Measures as NPDES Permit Terms. . . . . . . . . . . . . 4-23
Approaches for Writing Site-Specific Permit Terms of the NMP. . . . . . . . . . . . 4-25
Changes to a Permitted CAFO’s NMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-28
Process for Review and Modification of the NMP . . . . . . . . . . . . . . . . . . . . . . . . 4-31
4.1.8. Agricultural Stormwater Exemption for Permitted CAFOs. . . . . . . . . . . . . . . . . . . . 4-34
Permitted Large CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-34
Permitted Small and Medium CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-35
4.1.9. Water Quality-Based Effluent Limitations and Standards. . . . . . . . . . . . . . . . . . . . . 4-35
Requirements for the Production Area of Large CAFOs . . . . . . . . . . . . . . . . . . . 4-36
Requirements for the Land Application Area of Large CAFOs . . . . . . . . . . . . . 4-36
4.2. Monitoring, Record-Keeping, and Reporting Requirements of NPDES Permits
for CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-37
4.2.1. Monitoring Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-37
4.2.2. Recordkeeping Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-38

NPDES Permit Writers’ Manual for CAFOs

4.2.3. Reporting Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-43
Annual Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-43
4.3. Special Conditions for All NPDES Permits for CAFOs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-45
4.3.1. Additional Special Conditions as Determined by the Permitting Authority. . . . 4-45
4.3.2. Duty to Maintain Permit Coverage until the CAFO is Properly Closed . . . . . . . . 4-46
Closure Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-46
4.3.3. Manure Transfer Requirements for Large CAFOs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-47
4.4. Standard Conditions of a CAFO NPDES Permit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-48
4.4.1. Types of Standard Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-48
Reference. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-51

5. Nutrient Management Planning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.1. EPA’s Nine Minimum Requirements for Nutrient Management. . . . . . . . . . . . . . . . . . . . . . . 5-2
5.1.1. Permitted Large CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
5.1.2. Permitted Small and Medium CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
5.1.3. Unpermitted Large CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
5.2. Developing Permit Terms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4
5.3. Adequate Manure, Litter, and Wastewater Storage, Including Procedures to
Ensure Proper Operation and Maintenance of the Storage
Facility 40 CFR Part 122.42(e)(i) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
5.3.1. Permit Terms for Adequate Storage of Manure, Litter, and Wastewater. . . . . . . . . . 5-6
5.3.2. Technical Information on Storage Structure Design, Construction,
Operation and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Design and Construction of Storage Structures. . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
O&M of Storage Structures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Monitoring and Recordkeeping. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
5.4. Mortality Management 40 CFR 122.42(e)(ii) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
5.4.1. Permit Terms for Mortality Management. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
5.4.2. Technical Information on Mortality Management and Disposal. . . . . . . . . . . . . . . 5-19
Animal Mortality Disposal Practices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
5.5. Clean Water Diversion 40 CFR Part 122.42(e)(1)(iii). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
5.5.1. Permit Terms for Clean Water Diversion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
5.6. Prevention of Direct Animal Contact with Waters of the U.S.
40 CFR Part 122.42(e)(1)(iv) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
5.6.1. Permit Terms for Prevention of Direct Animal Contact with Waters of
the U.S.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
5.7. Chemical Disposal 40 CFR Part 122.42(e)(1)(v). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26

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5.7.1. Permit Terms for Chemical Disposal. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
5.7.2. Technical Information on Chemical Disposal. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28
5.8. Site-Specific Conservation Practices 40 CFR Part 122.42(e)(1)(vi). . . . . . . . . . . . . . . . . . . . . 5-29
5.8.1. Permit Terms for Conservation Practices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-29
5.8.2. Required Land Application Setback and Alternatives for Large CAFOs
40 CFR Part 412.4(c)(5). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-32
35-Foot Vegetated Buffer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-33
Demonstration That the Setback is Not Necessary. . . . . . . . . . . . . . . . . . . . . . . . 5-33
5.8.3. Additional Conservation Practices Identified in the NMP. . . . . . . . . . . . . . . . . . . . 5-34
5.9. Manure and Soil Testing Protocols 40 CFR Part 122.42(e)(1)(vii). . . . . . . . . . . . . . . . . . . . . . 5-35
5.9.1. Permit Terms for Protocols for Manure and Soil Testing . . . . . . . . . . . . . . . . . . . . . . 5-35
5.9.2. Technical information for Protocols for Manure and Soil Testing. . . . . . . . . . . . . . 5-36
Manure Test Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
Soil Test Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-42
5.10. Protocols for Land Application 40 CFR Part 122.42(e)(1)(viii). . . . . . . . . . . . . . . . . . . . . . . . . 5-47
5.11. Recordkeeping 40 CFR Parts 122.42(e)(1)(ix) and (e)(2) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-47
5.12. Developing an NMP. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-49
5.12.1. USDA’s Comprehensive Nutrient Management Plan. . . . . . . . . . . . . . . . . . . . . . . . . 5-49
5.12.2. Technical Assistance for Preparing NMPs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-50
5.12.3. NMPs Developed by Certified Specialists. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-51
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-52

6. Protocols for Land Application of Manure Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.1. Soil and Plant Availability of Nutrients. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.1.1. Nitrogen Cycle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.1.2. Phosphorus Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
6.1.3. Soil Fertility. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
6.2. Using Manure Nutrients. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
6.3. Standards for Nutrient Management. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-11
6.3.1. EPA’s State Requirements for Land Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-12
Requirements for State Technical Standards. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-12
6.4.

EPA’s CAFO Requirements for Land Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-17
A Note on the Orientation of Chapter 6:. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-18

6.5. Protocols for Land Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-18
6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches. . . . . . . . . . . . . . . . . . . 6-20
Fields Available for Land Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-21

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Timing Limitations for Land Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-22
Outcome of the Field-Specific Assessment of the Potential for Nitrogen
and Phosphorus Transport from Each Field. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-22
Planned Crop or Other Use. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-32
Realistic Annual Yield Goals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-34
Total Nitrogen and Phosphorus Recommendations for Each Crop. . . . . . . . . 6-35
6.5.2. Additional Site-Specific Terms: Linear Approach. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-39
Credits for Plant Available Nitrogen in the Field. . . . . . . . . . . . . . . . . . . . . . . . . 6-39
Consideration of Multi-Year Phosphorus Application . . . . . . . . . . . . . . . . . . . . 6-41
Accounting for All Other Additions of Plant Available Nitrogen and
Phosphorus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-42
Form and Source of Manure that Is Land Applied. . . . . . . . . . . . . . . . . . . . . . . . 6-43
Timing and Method of Land Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-44
The Maximum Amount of Nitrogen and Phosphorus from Manure,
Litter and Process Wastewater. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-51
The Methodology to Account for the Amount of Nitrogen and
Phosphorus in the Manure to be Applied. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-53
6.5.3. Additional Site-Specific Terms: Narrative Rate Approach. . . . . . . . . . . . . . . . . . . . 6-53
The Maximum Amounts of Nitrogen and Phosphorus from All Sources. . . . . 6-54
Alternative Crops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-56
The Methodology by which the NMP Calculates the Amount of
Manure to be Land Applied . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-57
6.5.4. Substantial Changes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-61
6.6. Permit Terms for Land Application Protocols Using a Sample NMP . . . . . . . . . . . . . . . . . 6-62
6.6.1. Site-Specific Terms: Linear and Narrative Rate Approaches. . . . . . . . . . . . . . . . . . 6-63
Fields Available for Land Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-63
Timing Limitations for Land Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-63
Outcome of the Assessment of the Potential for Nutrient and
Phosphorus Transport for Each Field. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-65
Planned Crops or Other Use (Fallow, Pasture, etc.) for Each Field and
Each Year. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-66
Realistic Annual Crop Yield Goal for Each Field. . . . . . . . . . . . . . . . . . . . . . . . . 6-66
Total Nitrogen and Phosphorus Recommendations for Each Crop by
Field and Year. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-67
6.6.2. Additional Site-Specific Terms: Linear Approach. . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-68
Credits for Plant Available Nitrogen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-68
Consideration of Multi-Year Phosphorus Application . . . . . . . . . . . . . . . . . . . . 6-69

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Accounting for All Other Additions of Plant Available Nitrogen and
Phosphorus to the Field. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-70
Form and Source of Manure that is Applied. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-70
Method and Timing of Land Application of Manure for Each Field . . . . . . . . . 6-71
Maximum Amount of Nitrogen and Phosphorus from Manure, Litter,
and Process Wastewater. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-72
Methodology to Account for the Amount of Nitrogen and Phosphorus
in the Manure to be Applied. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-73
6.6.3. Additional Site-Specific Terms: Narrative Rate Approach. . . . . . . . . . . . . . . . . . . . . 6-75
Maximum Amount of Nitrogen and Phosphorus from All Sources
of Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-75
Alternative Crops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-76
Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-76
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-96

Glossary
Appendix A. Basic Soil Science and Soil Fertility
Appendix B: Example Letters to Owners/Operators After a Site Visit
Appendix C: Example NPDES CAFO Permit Annual Report Form
Appendix D: Example Nutrient Management Plan Recordkeeping Forms
Appendix E: Minimum Depth of Rain at Which Runoff Begins
Appendix F: Voluntary Alternative Performance Standards for CAFOs
Appendix G. Winter Spreading Technical Guidance
Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist
Appendix I. NPDES CAFO Technical Standard Review Checklist
Appendix J: NPDES General Permit Template for CAFOs
Appendix K: NRCS Conservation Practice Standards
Appendix L: Nutrient Management Planning Software
Appendix M: Nutrient Management Recordkeeping Calendar Template
Appendix N: References for NPDES Permit Writers
Appendix O: Sample Site-Specific NPDES General Permit
Appendix P: Sample Nutrient Management Plan

NPDES Permit Writers’ Manual for CAFOs

Figures
Figure 1-1. U.S. AFOs, CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Figure 4-1. Process for Review and Modification of the Nutrient Management Plan . . . . . . . . . . . . . . . . . . 4-32
Figure 4-2. Process for Review and Modification of the Nutrient Management Plan (detail). . . . . . . . . . . 4-32
Figure 5-1. Cross section of properly designed lagoon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Figure 5-2. Schematic of Lagoon Depth Marker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
Figure 5-3. Sampling soil by type or condition. Within each field, collect a separate sample from
each area that has a different type of soil or different management history. . . . . . . . . . . . . . . . 5-36
Figure 6-1. The Nitrogen Cycle.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Figure 6-2. The Phosphorus Cycle.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Figure 6-3. The relationship between the phosphorus solution and the active pool. . . . . . . . . . . . . . . . . . . . 6-5
Figure 6-4. Excess manure nitrogen.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-10
Figure 6-5. Excess manure phosphorus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-10
Figure 6-6. Percent of soils testing medium or low in phosphorus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-11
Figure 6-7. Yield response curve illustrating the soil test interpretation levels.. . . . . . . . . . . . . . . . . . . . . . . 6-37
Figure 6-8. Removal rates versus fertilizer recommendations.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-37
Figure 6-9. An illustration of a 5-year NMP for a corn-soybean rotation.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-55
Figure 6-10. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-61

Tables
Table 2-1.

Large CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6

Table 2-2.

Medium CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9

Table 2-3.

Example factors for case-by-case CAFO designation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14

Table 3-1

Information required on NPDES application forms 1 and 2B . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

Table 4-1.

Elements of an NPDES Permit for a CAFO. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1

Table 4-2.

Effluent limitation summary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3

Table 4-3.

Applicability of NSPS for NPDES permits issued to CAFOs in subparts C and D after
promulgation of the revised CAFO regulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6

Table 4-4.

Numeric effluent limitations for subpart B—Ducks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9

Table 4-5.

Facilities where the technology-based limits must be developed using BPJ. . . . . . . . . . . . . . . 4-17

Table 4-6.

Required records for permitted Large CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-39

Table 4-7.

Required records for permitted Small and Medium CAFOs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-42

Table 5-1.

EPA minimum practice/NRCS conservation practice comparison . . . . . . . . . . . . . . . . . . . . . . . . 5-8

Table 5-2.

EPA minimum practice/NRCS Conservation practice comparison. . . . . . . . . . . . . . . . . . . . . . . 5-19

Table 5-3.

Poultry and livestock mortality rates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20

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Table 5-4.

Environmental risks of common mortality disposal practices. . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23

Table 5-5.

EPA minimum practice/NRCS conservation practice comparison . . . . . . . . . . . . . . . . . . . . . . . 5-25

Table 5-6.

EPA minimum practice/NRCS conservation practice comparison . . . . . . . . . . . . . . . . . . . . . . . 5-26

Table 5-7.

Example NMP provisions for chemical handling and disposal. . . . . . . . . . . . . . . . . . . . . . . . . . . 5-27

Table 5-8.

EPA minimum practice/NRCS conservation practice comparison . . . . . . . . . . . . . . . . . . . . . . . 5-28

Table 5-9.

Life spans for selected NRCS conservation practice standards. . . . . . . . . . . . . . . . . . . . . . . . . . . 5-31

Table 5-10. EPA minimum practice/NRCS conservation practice comparison . . . . . . . . . . . . . . . . . . . . . . . 5-32
Table 5-11. Example site-specific records to document NMP implementation. . . . . . . . . . . . . . . . . . . . . . . . 5-47
Table 5-12. USDA CNMP elements/NPDES NMP minimum practices comparison . . . . . . . . . . . . . . . . . . . 5-50
Table 6-1.

Manure nutrient content factors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8

Table 6-2.

Nutrient uptake parameters for selected crops used to estimate the assimilative
capacity of cropland. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8

Table 6-3.

Field-specific land application protocol terms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-20

Table 6-4.

General mineralization rates for nitrogen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-40

Table 6-5.

Legume nitrogen credits for Montana. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-41

Table 6-6.

Percentage of nitrogen in applied manure still potentially available to the soil
(ammonia volatilization causes the predicted losses) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-46

Glossary - 1

NPDES Permit Writers’ Manual for CAFOs

NPDES CAFO Permitting Glossary
25-year, 24-hour rainfall event – Mean precipitation event with a probable recurrence interval of
once in twenty-five years, as defined by the National Weather Service in Technical Paper No. 40,
“Rainfall Frequency Atlas of the United States,” May, 1961, or equivalent regional or State rainfall
probability information developed from this source.
100-year, 24-hour rainfall event – Mean precipitation event with a probable recurrence interval
of once in one hundred years, as defined by the National Weather Service in Technical Paper
No. 40, “Rainfall Frequency Atlas of the United States,” May, 1961, or equivalent regional or State
rainfall probability information developed from this source.
303(d) water body – Under section 303(d) of the 1972 Clean Water Act, states, territories, and
authorized tribes are required to develop lists of impaired waters. These impaired waters do not
meet water quality standards that states, territories, and authorized tribes have set for them. The
law requires that these jurisdictions establish priority rankings for waters on the lists and develop
TMDLs for these waters.
Aboveground storage tank – Aboveground storage tanks are used as an alternative to under
building pit storage and earthen basins. Current assembly practices for aboveground storage
facilities are primarily circular silo types and round concrete designs, but the structures may
also be rectangular. Such tanks are suitable for operations handling slurry (semisolid) or liquid
manure; this generally excludes open-lot waste which is inconsistent in composition and has a
higher percentage of solids. Below and aboveground storage tanks are appropriate in situations
where the production site has karst terrain, space constraints, or aesthetics issues associated
with earthen basins. Storing manure in prefabricated or formed storage tanks is especially
advantageous on sites with porous soils or fragmented bedrock. Such locations may be unfit for
earthen basins and lagoons because seepage and ground water contamination may occur.
Acre – 1 acre = 43,560 sq. ft. = 208.7 ft.; 2 = 0.405 hectares; or 640 acres = 1 sq. mile (called a
section).

NPDES CAFO Permitting Glossary

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NPDES Permit Writers’ Manual for CAFOs

Acre-foot – The volume of water that would cover one acre of land (43,560 square feet) to a depth
of one foot, equivalent to 325,851 gallons of water.
Aerobic – Living, active, or occurring only in the presence of free oxygen.
Air Quality Standards – Federal and state government-prescribed levels of a pollutant in the out­
side air that cannot be exceeded during a specified period of time in a specified geographical area.
Agronomy – The science of crop production and soil management.
Anaerobic (anoxic) – In the absence of oxygen.
Anaerobic digestion – A biological process that occurs in the absence of oxygen. In very large
animal production operation, it is sometimes used to produce biogas (a low energy gas which is a
combination of methane and carbon dioxide) from the biodegradable organic portion of manure.
This gas can be used as an energy source. After anaerobic digestion, the remaining semi-solid
(which is relatively odor free but still contains most of its nutrients) can be used as a fertilizer.
Apatite rock – A group of phosphate minerals, usually referring to hydroxyapatite, flouroapatite,
chloroapatite and bromapatite, named for the high concentrations of OH-, F-, Cl-, or Br- ions,
respectively, in the crystal. The formula of the admixture of the four most common endmembers
is written as Ca10(PO4)6(OH, F, Cl, Br)2, and the crystal unit cell formulae of the individual minerals
are written as Ca10(PO4)6(OH)2, Ca10(PO4)6(F)2, Ca10(PO4)6(Cl)2 and Ca10(PO4)6(Br)2.
Backgrounding – Growing program for feeder cattle from time calves are weaned until they are
on a finishing ration in the feedlot.
Basin – A tract of land in which the ground is broadly tilted toward a common point. Water that
falls onto any portion of the basin is carried toward the common point by a single river system.
Bedding – Material such as straw, sawdust, wood shavings, shredded newspaper, sand or other
similar material used in animal confinement areas for the comfort of the animal or to absorb
excess moisture. Bedding can drastically affect the characteristics of the manure, and must be
taken into consideration in the design of the storage facility.
Belowground storage tanks – Belowground storage tanks are used as an alternative to under
building pit storage and earthen basins. Belowground storage can be located totally or partially
below grade and should be surrounded by fences or guardrails to prevent people, livestock, or
equipment from accidently entering the tank. Such tanks are suitable for operations handling
slurry (semisolid) or liquid manure; this generally excludes open-lot waste which is inconsistent
in composition and has a higher percentage of solids. Below and aboveground storage tanks
are appropriate in situations where the production site has karst terrain, space constraints, or
aesthetics issues associated with earthen basins. Storing manure in prefabricated or formed
storage tanks is especially advantageous on sites with porous soils or fragmented bedrock.
Such locations may be unfit for earthen basins and lagoons because seepage and ground water
contamination may occur.

NPDES CAFO Permitting Glossary

Glossary - 3

NPDES Permit Writers’ Manual for CAFOs

Best Available Technology Economically Achievable (BAT) – Technology-based standard
established by the Clean Water Act (CWA) as the most appropriate means available on a national
basis for controlling the direct discharge of toxic and nonconventional pollutants to navigable
waters. BAT effluent limitations guidelines, in general, represent the best existing performance
of treatment technologies that are economically achievable within an industrial point source
category or subcategory.
Best Conventional Pollutant Control Technology (BCT) – Technology-based standard for
the discharge from existing industrial point sources of conventional pollutants including
BOD, TSS, fecal coliform, pH, oil and grease. The BCT is established in light of a two-part “cost
reasonableness” test which compares the cost for an industry to reduce its pollutant discharge
with the cost to a POTW for similar levels of reduction of a pollutant loading. The second test
examines the cost-effectiveness of additional industrial treatment beyond BPT. EPA must find
limits which are reasonable under both tests before establishing them as BCT.
Best management practice (BMP) – Permit condition used in place of or in conjunction with
effluent limitations to prevent or control the discharge of pollutants. May include schedule of
activities, prohibition of practices, maintenance procedure, or other management practice. BMPs
may include, but are not limited to, treatment requirements, operating procedures, or practices to
control runoff, spillage, leaks, or drainage from raw material storage.
Best professional judgment (BPJ) – The method used by permit writers to develop technologybased NPDES permit conditions, in those circumstances where there is no applicable effluent
limitation guideline, on a case-by-case basis using all reasonably available and relevant data.
Biochemical Oxygen Demand (BOD) – Laboratory measurement of the amount of oxygen
consumed by microorganisms while decomposing organic matter in a product. BOD levels are
indicative of the effect of the waste on fish or other aquatic life which require oxygen to live, and
though not a specific compound, it is defined as a conventional pollutant under the federal Clean
Water Act.
BOD5 – The amount of dissolved oxygen consumed in five days by biological processes breaking
down organic matter.
Boar – An uncastrated male hog.
Breeding stock – Sexually mature male and female livestock that are retained to produce
offspring.
Broiler – Meat-type chicken typically marketed at 6.5 weeks of age. Live weight at market
generally averages 4 to 4.5 pounds per bird.
Buffer Zone – The region near the border of a protected area; a transition zone between areas
managed for different objectives.
Buck – Male goat. Male goats are at times disparagingly called “Billy goats”.

NPDES CAFO Permitting Glossary

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NPDES Permit Writers’ Manual for CAFOs

Bull – Bovine male, uncastrated of breeding age.
Bushel – A dry volume measure of varying weight for grain, fruit, etc., equal to four pecks or eight
gallons (2150.42 cubic inches). A bushel of wheat, soybeans, and white potatoes each weighs 60
pounds. A bushel of corn, rye, grain sorghum, and flaxseed each weighs 56 pounds. A bushel of
barley, buckwheat, and apples each weighs 48 pounds.
By-product – Product of considerably less value than the major product. For example, the hide
and offal are by-products while beef is the major product.
Bypass – The intentional diversion of waste streams from any portion of a treatment (or
pretreatment) facility.
Calf – Young male or female bovine animal under 1 year of age.
Calve – Giving birth to a calf.
Capon – Castrated male chicken.
Coliform Bacteria – Microorganisms which typically inhabit the intestines of warm-blooded
animals. They are commonly measured in drinking water analyses to indicate pollution by
human or animal waste.
Compost – Decomposed organic material resulting from the composting process. Used to enrich
or improve the consistency of soil.
Conservation district – Any unit of local government formed to carry out a local soil and water
conservation program.
Conservation plan – A combination of land uses and farming practices to protect and improve
soil productivity and water quality, and to prevent deterioration of natural resources on all or
part of a farm. Plans may be prepared by staff working in conservation districts and must meet
technical standards. For some purposes, such as conservation compliance, the plan must be
approved by the local conservation district. Under the 1996 FAIR Act, conservation plans for
conservation compliance must be both technically and economically feasible.
Conservation practice (NRCS) – Any technique or measure used to protect soil and water
resources for which standards and specifications for installation, operation, or maintenance
have been developed. Practices approved by USDA’s Natural Resources Conservation Service are
compiled at each conservation district in its field office technical guide.
Conservation Reserve Enhancement Program (CREP) – A sub program of the Conservation
Reserve Program, CREP is a state-federal multi-year land retirement program developed by states
and targeted to specific state and nationally significant water quality, soil erosion, and wildlife
habitat problems. The CREP offers higher payments per acre to participants than the CRP, and
perhaps other benefits as well. States with approved programs include Maryland, Minnesota,
Illinois, New York, Oregon, Washington, and North Carolina.

NPDES CAFO Permitting Glossary

NPDES Permit Writers’ Manual for CAFOs

Glossary - 5

Conservation Reserve Program (CRP) – A USDA program, created in the Food Security Act of
1985, to retire from production up to 45 million acres of highly erodible and environmentally
sensitive farmland. Landowners who sign contracts agree to keep retired lands in approved
conserving uses for 10-15 years. In exchange, the landowner receives an annual rental payment,
cost-share payments to establish permanent vegetative cover and technical assistance.
Conservation tillage – Any tillage and planting system that leaves at least 30% of the soil surface
covered by residue after planting. Conservation tillage maintains a ground cover with less
soil disturbance than traditional cultivation, thereby reducing soil loss and energy use while
maintaining crop yields and quality. Conservation tillage techniques include minimum tillage,
mulch tillage, ridge tillage, and no- till.
Confinement area – The animal confinement area includes but is not limited to open lots, housed
lots, feedlots, confinement houses, stall barns, free stall barns, milk rooms, milking centers,
cowards, barnyards, medication pens, walkers, animal walkways, and stables.
Containment – Structures used to control runoff of precipitation that comes into contact with
manure, feed and other wastes on open feedlots. Examples of containment structures are lagoons
and holding ponds.
Contour farming – Field operations such as plowing, planting, cultivating, and harvesting on the
contour, or at right angles to the natural slope to reduce soil erosion, protect soil fertility, and use
water more efficiently.
Cover crop – A close-growing crop grown to protect and improve soils between periods of regular
crops.
Cow – Sexually mature female bovine animal that has usually produced a calf.
Cow-calf operation – A ranch or farm where cows are raised and bred mainly to produce calves
usually destined for the beef market. The cows produce a calf crop each year, and the operation
keeps some heifer calves from each calf crop for breeding herd replacements. The rest of the calf
crop is sold between the ages of 6 and 12 months along with old or nonproductive cows and bulls.
Such calves often are sold to producers who raise them as feeder cattle.
Critical Storage Period – The number of continuous days manure and wastewater cannot be
land applied or otherwise used. This occurs during the winter months or during the crop growing
season when application cannot be made.
Crop rotation – The growing of different crops, in recurring succession, on the same land in
contrast to monoculture cropping. Rotation usually is done to replenish soil fertility and to reduce
pest populations in order to increase the potential for high levels of production in future years.
Crop Year – The period of time it takes to go from one harvest to the next harvest. A crop year can
approximate a calendar year in length, if crops are only planted once per year. However, in some
climates there can be two crop years within a calendar year.

NPDES CAFO Permitting Glossary

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NPDES Permit Writers’ Manual for CAFOs

Dewatering – The removal of the liquid fraction from manure slurries. This is often done to
maximize storage by increasing the solids concentration or to facilitate the transportation of the
manure. Dewatering is often accomplished by mechanical separation (screen separator, beltpress, centrifuge) or gravity separation (settling basin).
Director – The Regional Administrator or State Director, as the context requires, or an authorized
representative. When there is no approved state program, and there is an EPA administered
program, Director means the Regional Administrator. When there is an approved state program,
“Director” normally means the State Director.
Digester – A vessel used for the biological, physical, or chemical break-down of livestock and
poultry manure.
Discharge – Discharge when used without qualification means the discharge of a pollutant.
Discharge of a pollutant means: (a) Any addition of any pollutant or combination of pollutants
to waters of the United States from any point source, or (b) Any addition of any pollutant or
combination of pollutants to the waters of the contiguous zone or the ocean from any point
source other than a vessel or other floating craft which is being used as a means of transportation.
This definition includes additions of pollutants into waters of the United States from: surface
runoff which is collected or channeled by man; discharges through pipes, sewers, or other
conveyances owned by a State, municipality, or other person which do not lead to a treatment
works; and discharges through pipes, sewers, or other conveyances, leading into privately owned
treatment works. This term does not include an addition of pollutants by any indirect discharger.
Dry cow – A cow that is not lactating.
Dry lot (dry operation) – An operation using confinement buildings and handling manure and
bedding exclusively as dry material, an operation using a building with a mesh or slatted floor
over a concrete pit, or an operation scraping manure to a covered waste storage facility is referred
to as a “dry” operation. When such practices are used, and are not combined with liquid manure
handling systems such as flushing to lagoons or storage ponds, these operations are referred to as
“other than liquid manure handling systems” or “dry” manure systems, or “dry” operations.
Duck – Term used to connote both sexes but is also used to refer to the female gender. Ducks are
typically marketed at 35 days of age at an average live weight of 7 pounds per bird.
Effluent – Water mixed with waste matter.
Effluent Limitations Guidelines (ELG) –Regulations issued by the EPA Administrator under
Section 304(b) of the Clean Water Act that establish national technology-based effluent
requirements for a specific industrial category.
Erosion – The wearing away of land surfaces by the action of wind or water.
Ephemeral stream – A stream that flows only sporadically, such as after storms.

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EQIP – The Federal Environmental Quality Incentive Program (EQIP) provides financial
assistance to producers to implement better conservation practices.
Ewe – A female sheep.
Evaporation pond – Used in regions where evaporation exceeds rainfall to separate manure
solids from liquids. Constructed to remove moisture from livestock manure.
Farm Service Agency – A division of the USDA that oversees the administration of all federal
farm programs. Programs include farm commodities, crop insurance, conservation programs
and farm loans. Offices are located in strategic counties in every state in the U.S. Formerly known
as ASCS, Agricultural Stabilization and Conservation Services.
Farrow-to-finish – Typically, a confinement operation where pigs are bred and raised to their
slaughter weight, usually 200–250 pounds.
Farrowing – Stage during which the pigs are born, and kept until they are weaned from the sow.
Fecal coliform bacteria – A group of bacteria found in the intestinal tract of humans and
animals, and also found in soil. While harmless in themselves, coliform bacteria are commonly
used as indicators of the presence of pathogenic organisms.
Feeder cattle – Cattle past the calf stage that have weight increased making them salable as
feedlot replacements.
Feedlot – Lot or building or a group of lots or buildings used for the confined feeding, breeding or
holding of animals. This definition includes areas specifically designed for confinement in which
manure may accumulate or any area where the concentration of animals is such that a vegetative
cover cannot be maintained. Lots used to feed and raise poultry are considered to be feedlots.
Pastures are not animal feedlots.
Fertilizer – Any organic or inorganic material, either natural or synthetic, used to supply
elements (such as nitrogen (N), phosphate (P2O5), and potash (K 2O)) essential for plant growth.
Filly – A female horse less than three years old.
Filter backwash – Reversing the flow of water back through the filter media to remove entrapped
solids.
Filter strips – An area of vegetation, generally narrow and long, that slows the rate of runoff,
allowing sediments, organic matter, and other pollutants that are being conveyed by the water to
be removed.
Finish pig – To feed a pig until it reaches market weight, 250–260 pounds.

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Finishing stage – Stage leading to and including full adulthood for swine is called the finishing
stage. The pigs remain here until they reach market weight, 240 to 260 pounds.
Flush system – In flush systems, large volumes of water flow down a sloped surface, scour
manure from the concrete, and carry it to a manure storage facility. There are three basic types
of flush systems: (1) under slat gutters, used primarily in beef confinement buildings and swine
facilities; (2) narrow-open gutters, used predominately in hog finishing buildings; and (3) wideopen gutters or alleys, most often seen in dairy free stall barns, holding pens, and milking parlors.
Forage Growth – All browse and non-woody plants that are eaten by wildlife and livestock.
Roughage of high feeding value. Grasses and legumes cut at the proper stage of maturity and
stored to preserve quality are forage. A crop that is high in fiber and grown especially to feed
ruminant animals.
Freeboard – The distance between the highest possible wastewater level in a manure storage/
treatment structure and the top edge of the structure.
Gelding – A castrated male horse.
Grassed waterway – Grassed waterways are areas planted with grass or other permanent
vegetative cover where water usually concentrates as it runs off a field. They can be either natural
or man-made channels. Grass in the waterway slows the water and can reduce gully erosion and
aid in trapping sediment.
Grazing land – Pasture, meadow, rangeland, or other similar area where livestock are put to feed
on the vegetation.
Ground water – The supply of fresh water found beneath the Earth’s surface, usually in aquifers,
which supply wells and springs.
Growing stage – Occurs after the piglets leave the nursery. Pigs are larger and better able to take
care of themselves at this stage, so larger group pens and a less controlled environment is needed.
They are kept here until they reach 120 to 140 pounds.
Gully erosion – Also called ephemeral gully erosion, this process occurs when water flows in
small channels and larger swales. Most gully erosion occurs on highly erodible soils, where there
is little or no crop residue cover, or where crop harvest disturbs the soil.
Heifer – Young female bovine cow prior to the time that she has produced her first calf.
Hen – Adult female chicken or turkey.
Herd – Group of cattle (usually cows) that are in a similar management program.
Highly erodible land (HEL) – Land that is very susceptible to erosion, including fields that have
at least 1/3 or 50 acres of soils with a natural erosion potential of at least 8 times their T value.

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Holding pond – A pond, usually made of earthen material, that is used to store manure
wastewater, or polluted runoff generally for a limited time.
Immobilization – When organic matter decomposes in soil and is absorbed by microorganisms
therefore, preventing it being accessible to plants.
Intermittent stream – Has flowing water only during certain periods of time, when groundwater
provides water for stream flow. During dry periods, intermittent streams may not have flowing
water. Runoff from rainfall or snowmelt is a supplemental source of water for the stream flow.
Irrigation – Applying water (or wastewater) to land areas to supply the water (and sometimes
nutrient) needs of plants. Techniques for irrigating include furrow irrigation, sprinkler irrigation,
trickle (or drip) irrigation, and flooding.
Irrigation return flow – Part of artificially applied water that is not consumed by plants or
evaporation, and that eventually ‘returns’ to an aquifer or surface water body, such as a lake or
stream.
Karst topography – An irregular limestone region with sinks, underground streams, and caverns.
Karst areas can provide direct channels for contaminants to reach the groundwater.
Kid – A young goat.
Lactation – Is the secretion of milk from the mammary glands and the period of time that a
female lactates to feed her young.
Lamb – A young sheep. An ewe lamb or ram lamb, depending upon the sex.
Land application – The removal of wastewater and waste solids from a control facility and
distribution to, or incorporation into the soil mantle primarily for beneficial reuse purposes.
Land application area – Land application area means land under the control of an AFO owner
or operator, whether it is owned, rented, or leased, to which manure, litter, or process wastewater
from the production area is or maybe applied.
Land-grant universities – State colleges and universities started from Federal government grants
of land to each state to encourage further practical education in agriculture, home economics,
and the mechanical arts.
Layer – Mature egg-type chicken over 32 weeks of age.
Legumes – A family of plants, including many valuable food, forage and cover species, such as
peas, beans, soybeans, peanuts, clovers, alfalfas, sweet clovers, lespedezas, vetches, and kudzu.
Sometimes referred to as nitrogen-fixing plants, they can convert nitrogen from the air to build
up nitrogen in the soil. Legumes are an important rotation crop because of their nitrogen-fixing
property.

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Liner – Any barrier in the form of a layer, membrane or blanket, naturally existing, constructed
or installed to prevent a significant hydrologic connection between liquids contained in retention
structures and waters of the United States.
Litter – A combination of manure and the bedding material placed in dry chicken production
facilities. The bedding material alone may also be referred to as litter.
Liquid manure – Usually less than 8.0% solids. Wash water, runoff, precipitation, and so forth are
added, if needed, to dilute the manure and lower the solids content.
Liquid manure handling system – An operation were animals are raised outside with swimming
areas or ponds, or with a stream running through an open lot, or in confinement buildings where
water is used to flush the manure to a lagoon, pond, or some other liquid storage structure.
Load allocation – Portions of a TMDL assigned to existing and future nonpoint sources, including
background loads.
Maintained – Animals are confined in the same area where waste is generated and/or
concentrated. Maintained can also mean that the animals in the confined area are watered,
cleaned, groomed, or medicated.
Manure – Fecal and urinary defecations of livestock and poultry; may include spilled feed,
bedding, or soil.
Manure storage area – The manure storage area includes but is not limited to lagoons, runoff
ponds, storage sheds, stockpiles, under house or pit storages, liquid impoundments, static piles,
and composting piles.
Mare – A mature female horse or pony.
Milking parlor – The area of a dairy where milking takes place.
Milking parlor wash water – Is water used to rinse the animals and equipment during the
milking process to improve sanitation. The wash water typically includes manure, feed solids,
hoof dirt along with detergents and disinfectants that are being used at the operation. The
amount of wash water used each day depends upon the number of animals milked and the
management practices followed.
Mineralization – When the chemical compounds in organic matter in soil decomposes or are
oxidized into plant-accessible forms.
Molt – A process during which hens stop laying and shed their feathers. Occurs naturally every
12 months or may be artificially induced.
Multi-year phosphorus application (phosphorus banking) – A practice that allows manure
application in a single year at rates in excess of the phosphorus requirements of the crops. In

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subsequent years, no phosphorus would be applied until the amount applied in the single year
has been removed through plant uptake and harvest.
National Institute of Food and Agriculture (NIFA) – NIFA’s unique mission is to advance
knowledge for agriculture, the environment, human health and well-being, and communities
by supporting research, education, and extension programs in the Land-Grant University
System and other partner organizations. NIFA does not perform actual research, education, and
extension but rather helps fund it at the state and local level and provides program leadership in
these areas
New discharger – Any building, structure, facility, or installation: (a) From which there is or may
be a discharge of pollutants; (b) That did not commence the discharge of pollutants at a particular
site prior to April 14, 2003; (c) Which is not a new source; and (d) Which has never received a
finally effective NDPES permit for discharges at that site.
New source – Any building, structure, facility, or installation from which there is or may be a
discharge of pollutants, the construction of which commenced:
a. After promulgation of standards of performance under Section 306 of the CWA which
are applicable to such source (i.e., February 12, 2003 for CAFOs); or
b. After proposal of standards of performance in accordance with Section 306 of the
CWA which are applicable to such source, but only if the standards are promulgated in
accordance with Section 306 of the CWA within 120 days of their proposal.
c. Except as otherwise provided in an applicable new source performance standard, a
source is a new source if it meets the definition in 40 CFR part 122.2; and
i. It is constructed at a site at which no other source is located; or
ii. It totally replaces the process or production equipment that causes the discharge of
pollutants at an existing source; or
iii. Its processes are substantially independent of an existing source at the same site. In
determining whether these processes are substantially independent, the Director
shall consider such factors as the extent to which the new facility is integrated with
the existing plant; and the extent to which the new facility is engaged in the same
general type of activity as the existing source.
New source performance standards (NSPS) – Technology-based standards for facilities that
qualify as new sources under 40 CFR parts 122.2, 122.29. Standards consider that the new source
facility has an opportunity to design operations to more effectively control pollutant discharges.
Nonpoint source – Diffuse pollution source (i.e. without a single point of origin or not introduced
into a receiving stream from a specific outlet). The pollutants are generally carried off the land by
storm water. Common non-point sources are agriculture, forestry, urban, mining, construction,
dams, channels, land disposal, saltwater intrusion, and city streets.

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No-Till farming – The soil is left undisturbed from harvest to planting except for nutrient and
seed injection. Weed control is accomplished primarily with herbicides.
Normal growing season – The time period, usually measured in days, between the last freeze
in the spring and the first frost in the fall. Growing seasons vary depending on local climate and
geography. It can also vary by crop as different plants have different freezing thresholds.
Nursery building – Used for the piglets after they are weaned. Pigs are kept in small groups
in this heated, well-insulated enclosure until they reach 60 to 80 pounds. A wire or other very
porous floor is used to maintain sanitary conditions. The nursery slotted phase is often broken
up into two growth stages, called, respectively, a “hot” and “cold” nursery, reflecting the room
temperatures used.
Nutrient – A substance that provides food or nourishment, such as usable proteins, vitamins,
minerals or carbohydrates. Fertilizers, particularly phosphorus and nitrogen, are the most
common nutrients that contribute to lake eutrophication and nonpoint source pollution.
Open lot – Pens or similar confinement areas with dirt, concrete, or other paved or hard surfaces
wherein animals or poultry are substantially or entirely exposed to the outside environment
except for small portions of the total confinement area affording protection by windbreaks or
small shed-type shade areas.
Other than a liquid manure handling system – An operation using confinement buildings with a
mesh or slatted floor over a concrete pit, where the manure is scraped into a waste storage facility,
or an operation using dry bedding on a solid floor. In this case the manure and bedding are not
combined with water for flushing to a storage structure.
Overflow – the discharge of manure or process wastewater resulting from the filling of wastewater
or manure storage structures beyond the point at which no more manure, process wastewater, or
storm water can be contained by the structure.
Pasture – Land used primarily for the production of domesticated forage plants, usually grasses
and legumes, for livestock (in contrast to rangeland, where vegetation is naturally-occurring and
is dominated by grasses and perhaps shrubs).
Permitting authority – The NPDES permit issuance authority that has been authorized under
part 123 of the Clean Water Act.
Pesticide – A chemical substance used to kill or control pests, such as weeds, insects, fungus,
mites, algae, rodents and other undesirable agents.
Phosphorus banking – See multi-year phosphorus application.
Pit system (deep) – Has a concrete floor and masonry or concrete side walls, is constructed
2–6 feet below the ground. The animal cages are then built 8 feet or more above the pit floor.
Because the pit is built below ground level, care must be taken to insure that surface and

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groundwater are not contaminated. Foundation drains and external grading to direct surface
water away help to keep manure dry, so that natural composting might occur. The most important
benefit of the deep-pit is that manure can be stored for several months or more.
Pit (shallow) – The most frequently used pit system. The concrete pit is 4–8 inches deep and is
located 3-6 feet below the cages. The manure and other waste is mechanically scraped or flushed
out with water to a storage area, or directly loaded into a spreader for direct field application.
Plate chiller water – Are used to cool milk being stored at the dairy. Condensation is formed on
the plates and drains from the chiller.
Point source – Any discernible, confined, and discrete conveyance, including but not limited
to any pipe, ditch, channel, tunnel, conduit, well, discrete fixture, container, rolling stock,
concentrated animal feeding operation, landfill leachate collection system, vessel, or other
floating craft from which pollutants are or may be discharged.
Pollutant – Dredged spoil, solid waste, incinerator residue, filter backwash, sewage, garbage,
sewage sludge, munitions, chemical wastes, biological materials, radioactive materials (except
those regulated under the Atomic Energy Act of 1954, as amended (42U.S.C. 2011 et seq.)),
heat, wrecked or discarded equipment, rock, sand, cellar dirt and industrial, municipal, and
agricultural waste discharged into water.
Pollution prevention – Identifying areas, processes, and activities which create excessive waste
products or pollutants in order to reduce or prevent them through, alteration, or eliminating a
process.
Poult – Young turkey, either male or female.
Process wastewater – Water directly or indirectly used in the operation of the CAFO for any or all
of the following: spillage or overflow from animal or poultry watering systems; washing, cleaning,
or flushing pens, barns, manure pits, or other CAFO facilities; direct contact swimming, washing,
or spray cooling of animals; or dust control. Process wastewater also includes any water which
comes into contact with any raw materials, products, or byproducts including manure, litter, feed,
milk, eggs, or bedding.
Process generated wastewater – See process wastewater.
Production area – That part of an AFO that includes the animal confinement area, the manure
storage area, the raw materials storage area, and the waste containment areas. The animal
confinement area includes but is not limited to open lots, housed lots, feedlots, confinement
houses, stall barns, free stall barns, milk rooms, milking centers, cow yards, barn yards,
medication pens, walkers, animal walkways, and stables. The manure storage area includes but
is not limited to lagoons, runoff ponds, storage sheds, stockpiles, under house or pit storages,
liquid impoundments, static piles, and composting piles. The raw materials storage area includes
but is not limited to feed silos, silage bunkers, and bedding materials. The waste containment

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area includes but is not limited to settling basins, and areas within berms and diversions which
separate uncontaminated storm water. Also included in the definition of production area is any
egg washing or egg processing facility, and any area used in the storage, handling, treatment, or
disposal of mortalities.
Post-harvest residue – That portion of a plant, such as a corn stalk, left in the field after harvest.
Pullet – Young female chicken between 10 and 32 weeks of age, usually this term denotes eggtype birds.
Ram – A male sheep which has not been castrated.
Rangeland – An open region over which livestock may roam and feed. The plant cover is
principally native grasses, grass like plants, and shrubs. It includes natural grasslands,
savannahs, certain shrubs and grass like lands, most deserts, tundra, alpine communities,
coastal marshlands, and wet meadows. It also includes lands that are re-vegetated naturally or
artificially and are managed like native vegetation.
Raw materials storage area – Includes but is not limited to feed silos, silage bunkers, and
bedding materials.
Retention facility or retention structure – All collection ditches, conduits and swales for the
collection of runoff and wastewater, and all basins, ponds, pits, tanks and lagoons used to store
wastes, wastewaters and manures.
Return flow – Surface and subsurface water that leaves the field following application of irrigation
water.
Rill erosion – An erosion process in which numerous small channels, typically a few inches deep,
are formed. It occurs mainly on recently cultivated soils or on recent cuts and fills.
Riparian – Pertaining to or situated on or along the bank of a stream or other body of water.
Riparian buffer – A strip of vegetation planted along the bank of a body of water which slows the
rate of flow of runoff from adjoining uplands, causing sediment and other materials to fall out
onto the land before the runoff enters and pollutes the body of water.
Roaster – Meat-type chicken marketed at 9 weeks for males and 11 weeks for females. Live weight
at market ranges between 6 and 8 pounds per bird.
Root zone – The depth of soil penetrated by plant roots.
Rotational grazing – Grazing two or more pastures in regular sequence, with rest periods for the
recovery of herbage.

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Ruminants – Hoofed animals with four-chambered stomachs (i.e. cattle, sheep, goats).Ruminants
have a complex digestive system with a complex biological system that is capable of generating
much of their own protein needs.
Runoff – That part of precipitation, snow melt, or irrigation water that runs off the land into
streams or other surface-water. It can carry pollutants from the air and land into receiving waters.
Sediment – Solid material that is in suspension, is being transported, or has been moved from its
original location by air, water, gravity or ice.
Sedimentation – The addition of soils to lakes, a part of the natural aging process, making lakes
shallower. The process can be greatly accelerated by human activities.
Semi-solid manure – Contains little bedding and usually no extra water added. In most cases,
little drying occurs before handling. During wet weather the manure scraped from open lots can
also be semi-solid in nature.
Settling basin – A basin, often concrete lined, that is a holding area for wastewater and runoff
where the heavier particles sink to the bottom. The remaining fraction is then moved to another
storage structure or utilized by the operation.
Silage – Forage, corn fodder, or sorghum preserved by partial fermentation. Silage is stored in airtight stacks, pits, bags or silos. It is generally used as a feed for cattle.
Sinkhole – A depression in the landscape where limestone has been dissolved.
Soil loss tolerance (‘T’ value) – For a specific soil, the maximum average annual soil loss
expressed as tons per acre per year that will permit current production levels to be maintained
economically and indefinitely. T values range from 2 to 5 tons per acre per year.
Soil survey – A program of the Natural Resource Conservation Service to inventory soil resources
as a basis for determining land capabilities and conservation treatments that are needed, provide
soil information to the public (primarily through maps), and provide technical support to those
who use soils information. About 90% of the private lands have been mapped.
Solid manure – Combination of urine, bedding, and feces with little or no extra water added. It is
usually found in loafing barns, calving pens, and open lots with good drainage.
Source-water protection area – The area delineated by a state for a Public Water Supply or
including numerous such suppliers, whether the source is ground water or surface water or both.
Sow – Female that has farrowed at least one litter.
Stallion – An unaltered (uncastrated) male horse.
Steer – Bovine male castrated prior to puberty.

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Stocker cattle – Heifers and/or steers that are being grown on pasture or other forage for later sale
as feedlot replacements.
Storage – Refers to the structures used to hold manure, litter, or process wastewater to reduce
the need for frequent hauling and land spreading, to allow land spreading at a time when soil
and climatic conditions are suitable, or to allow nutrient application at or near the crop’s growing
season.
Storage pond – A liquid impoundment used to hold manure and wastewater.
Stripcropping – Growing crops in a systematic arrangement of strips or bands, usually parallel to
the land’s contour, that serve as barriers to wind and water erosion.
T value (or T level) – For a specific soil, the maximum average annual soil loss expressed as tons
per acre per year that will permit current production levels to be maintained economically and
indefinitely; the soil loss tolerance level.
Technology-based effluent limit – A permit limit for a pollutant that is based on the capability of
a treatment method to reduce the pollutant to a certain concentration.
Terrace – An embankment, ridge, or leveled strip constructed across sloping soils on the contour,
or at right angle to the slope. The terrace intercepts surface runoff so that it can soak into the soil
or flow slowly to a prepared outlet, decreasing rates of soil erosion.
Tile drain – Lines of concrete, clay, fiber, plastic or other suitable material pipe placed in the
subsoil to collect and drain water from the soil to an outlet. Infiltrated water that is captured by
drain tiles is usually diverted to surface water.
Tom – Male turkey.
Total Suspended Solids – A measure of the material suspended in wastewater. Total suspended
solids (TSS) cause: (1) interference with light penetration, (2) buildup of sediment and
(3) potential reduction in aquatic habitat. Solids also carry nutrients that cause algal blooms and
other toxic pollutants that are harmful to fish.
Treatment pond/lagoon – An impoundment made by excavating or earth fill to biologically treat
manure and wastewater.
Upset – An exceptional incident in which there is unintentional and temporary noncompliance
with the permit limit because of factors beyond the reasonable control of the permittee. An upset
does not include noncompliance to the extent caused by operational error, improperly designed
treatment facilities, inadequate treatment facilities, lack of preventive maintenance, or careless or
improper operation.
Veal – Meat from very young cattle (under 3 months of age). Veal typically comes from dairy bull
calves.

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Wasteload allocation – The proportion of a receiving water’s total maximum daily load that is
allocated to one of its existing or future point sources of pollution.
Wastewater – Water containing waste or contaminated by waste contact, including processgenerated and contaminated rainfall runoff.
Water quality standard (WQS) – A law or regulation that consists of the beneficial use or uses of a
waterbody, the numeric and narrative water quality criteria that are necessary to protect the use
or uses of that particular waterbody, and an antidegradation statement.
Water quality-based effluent limit – A value determined by selecting the most stringent of the
effluent limits calculated using all applicable water quality criteria (e.g., aquatic life, human
health, and wildlife) for a specific point source to a specific receiving water for a given pollutant.
Water table – The top surface of the aquifer nearest ground level.
Waters of the United States – Waters of the United States or waters of the U.S. means:
(a) All waters which are currently used, were used in the past, or may be susceptible to
use in interstate or foreign commerce, including all waters which are subject to the ebb
and flow of the tide;
(b) All interstate waters, including interstate wetlands;
(c) All other waters such as intrastate lakes, rivers, streams (including intermittent
streams), mudflats, sand flats, wetlands, sloughs, prairie potholes, wet meadows, playa
lakes, or natural ponds the use, degradation, or destruction of which would affect or
could affect interstate or foreign commerce including any such waters:
(1) Which are or could be used by interstate or foreign travelers for recreational or
other purposes;
(2) From which fish or shellfish are or could be taken and sold in interstate or foreign
commerce; or
(3) Which are used or could be used for industrial purposes by industries in interstate
commerce;
(d) All impoundments of waters otherwise defined as waters of the United States under
this definition;
(e) Tributaries of waters identified in paragraphs (a) through (d) of this definition;
(f) The territorial sea; and
(g) Wetlands adjacent to waters (other than waters that are themselves wetlands)
identified in paragraphs (a) through (f) of this definition.
Waste treatment systems, including treatment ponds or lagoons designed to meet the
requirements of CWA (other than cooling ponds as defined in 40 CFR part 423.11(m)

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which also meet the criteria of this definition) are not waters of the United States. This
exclusion applies only to manmade bodies of water which neither were originally created
in waters of the United States (such as disposal area in wetlands) nor resulted from the
impoundment of waters of the United States. Waters of the United States do not include
prior converted cropland. Notwithstanding the determination of an area’s status as prior
converted cropland by any other federal agency, for the purposes of the Clean Water Act,
the final authority regarding Clean Water Act jurisdiction remains with EPA.
Watershed – The surrounding land area that drains into a lake, river or river system.
Wet lot – Wet system, or liquid manure handling system.
Wetlands – A lowland area, such as a marsh, bog, swamp, or similar saturated with water.
Wetlands are crucial wildlife habitat, and important for flood control and maintaining the health
of surrounding ecosystems.
Yield – The number of bushels (or pounds or hundred weight) that a farmer harvests per acre.

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Chapter

1

1. Introduction
1.1. Overview
The NPDES Permit Writers’ Manual for Concentrated Animal Feeding Operations provides
information to National Pollutant Discharge Elimination System (NPDES) permit writers on
permitting requirements for Concentrated Animal Feeding Operations (CAFOs). The information
in the Manual may also be useful for inspectors, facility operators, and the general public. The
Manual replaces the 2003 Permit Writers’ Guidance Manual and Example NPDES Permit for
Concentrated Animal Feeding Operations. The new version reflects the current NPDES regulations
and Effluent Limitation Guidelines (ELGs) applicable to CAFOs under the Clean Water Act (CWA),
including revisions to the regulations that the U.S. Environmental
Protection Agency (EPA) finalized and published in the Federal
Register (FR) in 2008.1 Those requirements are collectively referred
to in this Manual as the CAFO regulations.
The Manual does not cover types of discharges from CAFOs that
trigger the requirement for a CAFO to apply for a NPDES permit.
This requirement commonly referred to as the “Duty-to-Apply”
requirement, will be covered in a stand-alone document. The
CWA establishes the basic structure for regulating discharges
of pollutants into the waters of the United States and setting
quality standards for surface waters. Under the CWA, it is
unlawful to discharge any pollutant from a point source
without an NPDES permit. The CWA defines point source to
include “any discernible, confined, and discrete conveyance,
including but not limited to any … concentrated animal
feeding operation … from which pollutants are or may be
discharged.”2 Under the NPDES CAFO regulations, a CAFO
that discharges must seek NPDES permit coverage.3

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NPDES Permit Writers’ Manual for CAFOs

1.2. Background
EPA began regulating the discharges of wastewater and manure from CAFOs in the 1970s. In
2003, the Agency updated the original CAFO regulations to address changes in the animal
agriculture industry sectors. 68 FR 7176 (Feb. 12, 2003). EPA subsequently published revisions
to the CAFO Rule in 2008 to address a 2005 decision by the U.S. Court of Appeals for the Second
Circuit in litigation challenging the 2003 regulatory updates.4 73 FR 70418 (Nov. 20, 2008).
At the time of the 2003 revised regulations, EPA estimated that animal feeding operations
(AFOs) annually produce more than 500 million tons of animal manure.5 This manure can pose
substantial risks to the environment and public health if managed improperly. EPA projected in
2003 that the revised rule would result in annual pollutant reductions of 56 million pounds of
phosphorus (P), 110 million pounds of nitrogen (N), and two billion pounds of sediment.
Today, there are slightly more than one million farms with livestock in the United States.6 EPA
estimates that about 212,000 of those farms are likely to be AFOs—operations where animals
are kept and raised in confinement. Although the number of AFOs has declined since 2003,
the total number of animals housed at AFOs has continued to grow because of expansion
and consolidation in the industry. As Figure 1-1 shows, EPA’s NPDES CAFO program tracking
indicates that 20,000 of those AFOs are CAFOs—AFOs that meet certain numeric thresholds or
other criteria—and that 8,000 of these CAFOs have NPDES permit coverage.7

Figure 1-1. U.S. AFOs, CAFOs

The CAFO regulations identify NPDES permitting requirements for AFOs that are classified as
CAFOs and that discharge. If CAFOs do not seek NPDES permit coverage, discharges from their
land application areas only qualify for the agricultural stormwater exemption if the CAFOs
implement and document basic nutrient management practices. EPA generally expects that
the nutrient management requirements are being followed when a CAFO has developed and
is implementing a comprehensive nutrient management plan (CNMP) in accordance with the
U.S. Department of Agriculture (USDA) guidance. For permitted CAFOs, nutrient management
1. Introduction
1.1. Overview

1.2. Background

1.3. Purpose and Organization of this
Manual

1.4. Limitations of this Manual

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NPDES Permit Writers’ Manual for CAFOs

plans developed and implemented as a condition of an NPDES permit must be based on applic­able
technical standards for nutrient management established by the NPDES permitting authority.8
The federal CAFO program is designed to support and complement an array of voluntary and
regulatory programs administered by USDA, EPA, and states (e.g., EQIP, Idaho One Plan, New
York’s AEM program). The CAFO regulations are an integral part of an overall federal strategy
to support a vibrant agricultural economy while simultaneously ensuring that all AFOs manage
their manure in a manner that is protective of the environment. EPA and USDA have worked
collaboratively to ensure that USDA’s voluntary programs and EPA’s regulatory and voluntary
programs complement each other and support effective nutrient management by all AFOs.
EPA and USDA will continue to coordinate the development and implementation of regulatory
and non-regulatory tools (e.g., software, guidance, conservation practices) to support both
agricultural and environmental protection goals.

1.3. Purpose and Organization of this Manual
This Manual provides information to NPDES permitting authorities on how to implement the
CWA NPDES regulations for CAFOs:
▶ Chapter 2 describes livestock operations that are regulated under the NPDES CAFO
program. This description covers how EPA which livestock operations are AFOs and
how, once an operation is defined as an AFO, it is then determined to be a CAFO.
As mentioned above, the manual does not cover when CAFOs need NPDES permit
coverage as this topic is covered in a separate EPA document.
▶ Chapter 3 discusses the two options NPDES permitting authorities have for issuing
NPDES permits for CAFOs: individual permits and general permits. It describes the
administrative process for both options and provides examples of situations in which
each option is most appropriate.
▶ Chapter 4 discusses the critical elements of an NPDES permit for a CAFO. Those
elements include effluent limitations and standards, monitoring, reporting and recordkeeping requirements, special conditions, and standard conditions. It provides a
detailed description of the requirements for each element and how to write a permit
with enforceable terms and conditions.
▶ Chapter 5 provides technical information on the nine basic components of a nutrient
management plan (NMP) as required by the NPDES CAFO regulations. It also provides
examples of permit terms reflecting the nine minimum measures.
▶ Chapter 6 focuses specifically on the portion of the NMP that establishes protocols for
land applying manure, litter, and process wastewater. It explains how to write permit
terms using the two approaches—linear and narrative—outlined in the NPDES CAFO
regulations.

1. Introduction
1.1. Overview

1.2. Background

1.3. Purpose and Organization of this
Manual

1.4. Limitations of this Manual

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NPDES Permit Writers’ Manual for CAFOs

The Manual assumes that the reader has a working knowledge of how NPDES permits are
developed. Permit writers should also be familiar with applicable state voluntary and regulat­
ory programs, and how those programs relate to the federal or state NPDES programs. The
appendices contain supplementary information that is relevant to CAFOs and CAFO permitting.
That information will also be of interest to CAFO owner/operators, the general public, and
permit writers.

1.4. Limitations of the Manual
Although the Manual provides clarification of NPDES CAFO regulatory requirements, it does not
alter or substitute for any of the NPDES CAFO regulations. The Manual, including the example
permit and example NMP, is not a rule, is not legally enforceable, and does not confer legal
rights or impose legal obligations on any federal or state agency or on any member of the public.
If a conflict is apparent between the Manual and any statute or regulation, the Manual is not
controlling. EPA has made every effort to ensure the accuracy of information in the Manual, but
obligations of the regulated community are determined by the relevant statutes, regulations, or
other legally binding requirements.
It is important to note that the Manual does not cover a CAFO’s “Duty-to-Apply” for NPDES
permit coverage. That topic was covered separately in prior EPA guidance, and EPA is at present
updating both the NPDES CAFO regulations as well as the related guidance to reflect the 2011
legal decision in litigation on this topic. See Nat’l Pork Producers Council v. EPA, 635 F.3d 738
(5th Cir. 2011). In that decision, the court vacated the requirement that CAFOs that propose to
discharge must apply for an NPDES permit, but upheld the duty to apply for discharging CAFOs.
Permit writers should be aware that other NPDES requirements besides CAFO requirements
may apply to CAFOs. For example, Chapter 4 discusses the need for NPDES stormwater permits.
In addition, states authorized to implement the NPDES permitting program have the option of
establishing more stringent NPDES requirements than those laid out in the federal regulations.9
The Manual does not cover NPDES requirements for live animal receiving and holding areas at
Meat and Poultry Processing (MPP) facilities. Those facilities are engaged in the slaughtering,
dressing, and packing of meat and poultry products and are not included in EPA’s definition of an
AFO. That industry is considered a different point source category and is covered by a separate set
of NPDES requirements connected with the ELG for the sector as laid out in 40 CFR part 432.
The word should as used in the Manual, including the example permit and example NMP,
does not connote a requirement, but it does indicate EPA’s recommendation for effective
implementation of legal requirements and protection of the environment. The Manual might not
apply in a situation according to the circumstances, and EPA, states and tribes have the discretion
to adopt approaches on a case-by-case basis that differ from the Manual. Permitting authorities
will make each permitting decision on a case-by-case basis and will be guided by the applicable

1. Introduction
1.1. Overview

1.2. Background

1.3. Purpose and Organization of this
Manual

1.4. Limitations of this Manual

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NPDES Permit Writers’ Manual for CAFOs

requirements of the CWA and implementing regulations, taking into account comments and
information presented at appropriate times by interested persons.
EPA may decide to revise the Manual without public notice. The public may offer suggestions to
EPA for clarifications at any time.

Endnotes
Title 40 of the Code of Federal Regulations (CFR) 122.23 et seq., as published in 73 Federal Register (FR) 70418.

1

CWA section 502(14)

2

40 CFR § 122.23(d)(1)

3

Waterkeeper Alliance et al. v. EPA, 399 F.3d 486 (2d Cir. 2005)

4

The term manure as used here and throughout the Manual refers to manure, litter, and process wastewater.

5

2007 U.S. Department of Agriculture Census of Agriculture

6

NPDES CAFO Rule Implementation Status—National Summary, Midyear 2011

7

See 40 CFR part 412.4(c)(2)

8

40 CFR § 123.25(a)

9

1. Introduction
1.1. Overview

1.2. Background

1.3. Purpose and Organization of this
Manual

1.4. Limitations of this Manual

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NPDES Permit Writers’ Manual for CAFOs

Chapter

2

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)
When Congress passed the CWA in 1972, it specifically included the term concentrated animal
feeding operation in the definition of point source. CWA § 502(14). Before EPA defined the CWA
term concentrated animal feeding operations in the 1976 CAFO regulations, the 1974 ELGs for
the Feedlots Point Source Category, formerly 40 CFR part 412.11(b), defined a feedlot to mean “a
concentrated, confined animal or poultry growing operation for meat, milk or egg production,
or stabling, in pens or houses wherein the animals or poultry are fed at the place of confinement
and crop or forage growth or production is not sustained in the area of confinement.” Similarly,
the support documentation for the ELG [see, for example, EPA’s Development Document for the
Final Revisions to the National Pollutant Discharge Elimination System Regulation and the Effluent
Guidelines for Concentrated Animal Feeding Operation, EPA-821-R-03-001 (2002)] distinguished
between animals grown in feedlots and those grown in non-feedlot situations. The development
document defines feedlot using the following three conditions:
1. A high concentration of animals held in a small area for periods in conjunction with
one of the following purposes:
a. Production of meat.
b. Production of milk.
c. Production of eggs.
d. Production of breeding stock.
e. Stabling of horses.
2. The transportation of feed to animals for consumption.
3. By virtue of the confinement of animals or poultry, the land or area will neither sustain
vegetation nor be available for crop or forage.

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NPDES Permit Writers’ Manual for CAFOs

In 1976 EPA revised its regulations in response to a court case holding that EPA could not
exempt certain categories of point sources from NPDES permit requirements. NRDC v. Train,
396 F. Supp. 1393 (D.D.C. 1975), aff’d NRDC v. Costle, 586 F.2d 1369 (D.C. Cir. 1977).The revised
regulations refer to CAFOs rather than feedlots. 41 FR 11458 (March 18, 1976). The 1976 rule
defined which facilities were CAFOs, and therefore point sources under the CWA, and established
permitting requirements for CAFOs. Id. EPA’s 1976 definition of CAFO draws on the definition of
a CAFO from the 1974 feedlot definition. Although the definition of the term CAFO was further
revised in the 2003 CAFO regulations, the types of facilities covered by the definition are nearly
identical to those in the original definition of a feedlot.
A facility must first meet the definition of an AFO before it can be considered a CAFO. AFOs are
defined as, “operations where animals have been, are, or will be stabled or confined and fed or
maintained for a total of 45 days or more in any 12-month period and where vegetation is not
sustained in the confinement area during the normal growing season.” 40 CFR § 122.23(b)(1).
EPA interprets maintained to mean that the animals are confined in the same area where waste
is generated or concentrated. Areas where animals are maintained can include areas where
animals are fed and areas where they are watered, cleaned, groomed, milked, or medicated. For
an overview of the livestock industry, see Chapter 4 of the Technical Development Document for
the 2003 CAFO regulations.

Regulatory Citation
Animal feeding operation (AFO) means a lot or facility (other than an aquatic animal
production facility) where the following conditions are met:
Animals have been, are or will be stabled or confined and fed or maintained for a
total of 45 days or more in any 12-month period.
AND
Crops, vegetation, forage growth, or post-harvest residues are not sustained in the
normal growing season over any portion of the lot or facility.
40 CFR § 122.23(b)(1)

The first part of the regulatory definition of an AFO means that animals must be kept on the lot or
facility for a minimum of 45 days in a 12-month period. If an animal is confined for any portion of
a day, it is considered to be on the facility for a full day. For example, dairy cows that are brought
in from pasture for less than an hour to be milked are counted as being confined (i.e., on the lot
or facility) for the day. In addition, the same animals are not required to remain on the lot for
45 days or more for the operation to be defined as an AFO. Rather, the first part of the regulatory
definition is met if some animals are fed or maintained on the lot or facility for 45 days out of
any 12-month period. The 45 days do not have to be consecutive, and the 12-month period does
not have to correspond to the calendar year. For example, June 1 to the following May 31 would
constitute a 12-month period. Therefore, animal operations such as stockyards, fairgrounds, and
auction houses where animals may not be fed, but are confined temporarily, may be AFOs.
2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)

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NPDES Permit Writers’ Manual for CAFOs

The second part of the regulatory definition of an AFO distinguishes confinement areas from
pasture or grazing land. That part of the definition relates to the portion of the facility where
animals are confined and where natural forage or planted vegetation does not occur during
the normal growing season. Confinement areas might have some vegetative growth along the
edges while animals are present or during months when animals are kept elsewhere. If a facility
maintains animals in an area without vegetation, such as dirt lots with incidental vegetative
growth, the facility meets the second part of the AFO definition.
True pasture and rangeland operations are not considered AFOs because animals at those
operations are generally maintained in areas that sustain crops or forage growth during the
normal growing season. In some pasture-based operations, animals can freely wander in and out
of areas for food or shelter; that is not considered confinement. In general, an area is a pasture
if vegetation is maintained during the normal growing season. However, pasture and grazingbased operations can also have confinement areas (e.g., feedlots, barns, milking parlors, pens)
that meet the definition of an AFO.
Incidental vegetation in a clear area of confinement would not exclude an operation from meeting
the definition of an AFO. In the case of a winter feedlot, the second part of the AFO definition
(i.e., no vegetation) is meant to be evaluated during the winter, when the animals are confined.
Animals from a grazing operation can be confined during winter months in a confinement area
that had vegetation during other parts of the year. If the animals are confined for more than
45 days but not year-round and vegetation emerges in the spring when animals are removed, the
presence of vegetation does not prevent that feedlot from being defined as an AFO because the
vegetation is growing when animals are not present. In that example, the feedlot will not sustain
the vegetation that had emerged in spring once the animals are moved back into the feedlot.
Therefore, the facility in the example meets the definition of an AFO.

Winter feeding of cattle. (Photo courtesy of USDA/NRCS)

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)

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NPDES Permit Writers’ Manual for CAFOs

Is this animal production operation an AFO?
Example A: An operation confines its animals for 10-day intervals every month for 5 months.
The animals are kept in an enclosure with slot floors.
Answer: The operation meets the AFO definition because it confines animals for a total of
50 days (i.e. more than 45 days) in a 12-month period, and the confinement area has slot
floors and therefore sustains no vegetation.
Example B: An operation confines mature animals in pens of five each. It has 200 pens per
building and five buildings. The animals are confined year-round.
Answer: The operation is an AFO because it confines animals for 45 days or more and does
not sustain vegetation in the confinement area.
Example C: An operation raises beef cattle in a 5,000-acre pasture from April 1 through
November 30 each year. From December 1 through March 3, the cattle are confined by a
fence to a 10-acre area. The animals are not free to move between the temporary confinement
area and the pasture area. The growing season for the area in which the operation is located
is from May 1 through October 15. A site visit is made to the operation during January, and
the 10-acre area where the animals are confined has vegetation on less than 5 percent of
the ground; the other areas are barren soil or packed manure. The confinement area was
completely covered by vegetation during a prior visit to the operation during August.
Answer: While the operation is pasture-based for most of the year, it meets the definition
of an AFO. The animals are held in confinement for more than 45 days, and the vegetation
has been denuded to the point that it is incidental while the animals are in confinement.
The fact that the vegetation reestablishes itself some time after the animals have been
released from confinement does not change the fact that the winter confinement results in
the operation meeting the definition of an AFO.
Example D: A beef cattle operation maintains the herd on pastures from March 15 through
November 15. From November 16 through March 14, the herd is moved to a fenced field
where crops were grown during the spring and summer. During the winter, while the animals
are confined to the field, the animals eat all the post-harvest residue and other vegetation that
remained in the field after the crops were harvested. Additional feed is also brought to the
field to sustain the herd throughout the winter.
Answer: The operation meets the AFO definition. The animals are confined and fed for more
than 45 days in a 12-month period (November through March). Although the confinement
area is used for crop production during times when the animals are grazing on pasture, the
vegetation is not sustained during the period when the animals are confined there.
Example E: An operation raises beef cattle in a 10,000-acre pasture rangeland. In the winter,
food is brought to various locations in the pasture rangeland to sustain the animals. The area
immediately around the food supply is rendered barren of vegetation. However, the animals
have full access to the pasture area.
Answer: The operation is not an AFO because the animals are free to move within the entire
pasture, and the vegetation is sustained in pasture areas.

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)

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NPDES Permit Writers’ Manual for CAFOs

Is this animal production operation an AFO? (continued)
Example F: An operation raises beef cattle in a 2,000-acre pasture. In the winter, the animals
congregate in a smaller area (e.g., 100 acres), and have access to a creek as their primary
source of water. The area immediately around the creek is rendered barren of vegetation when
the animals are present. The barren area constitutes approximately 10 percent of the 100-acre
wintering area. The remainder of the 100 acres retains vegetative cover.
Answer: The operation is not an AFO because vegetation is sustained in the confinement
area while the animals are present. While the practices at the operation do not result in
it meeting the definition of an AFO, the practices are not protective of water quality. EPA
would encourage such an operation to provide an alternative water source to keep the
animals out of the creek to reduce potential water quality impacts.
Example G: An operation raises cattle on pasture; however, a number of the cattle are
confined for birthing each spring. The confinement area is a dirt-floored pen that has only
incidental vegetation along the edges and in some small areas in the pen. The animals are in
the pen for 90 days each spring.
Answer: The operation meets the AFO definition. The animals are confined and fed for more
than 45 days, and the vegetation in the confinement area is only incidental.
Example H: An operation raises cattle on pasture; however, as part of the rotational grazing
program the cattle frequently are moved between smaller, fenced pasture areas. Cattle move
between pastures in narrow laneways that are largely devoid of vegetation. The barren area
constitutes less than 10 percent of the pasture areas, and the remainder of the acres retains
vegetative cover year-round. The animals are not fed or watered in the laneways and are
prevented from congregating in the laneways by gates and fencing.
Answer: The operation does not meet the AFO definition. The animals are not confined in
the laneways that are devoid of vegetation.

2.2. Concentrated Animal Feeding Operations (CAFOs)
This section provides information to help identify which AFOs are CAFOs. An AFO is a CAFO if
it meets the regulatory definition of a Large or Medium CAFO, 40 CFR parts 122.23 (b)(4) or (6),
or has been designated as a CAFO, 40 CFR part 122.23(c), by the NPDES permitting authority or
by EPA (see Section 2.2.8). Note that some authorized states have adopted regulatory definitions
for CAFOs that are more inclusive and, therefore, broader in scope than EPA’s regulations. Those
facilities are subject to requirements under state law but not under federal law.

2.2.1. Types of Animal Operations Covered by CAFO
Regulations
The CAFO regulations define a Large CAFO on the basis of the number of animals confined.
Medium CAFOs are defined as meeting specific criteria in addition to the number of animals
confined, and those criteria are discussed in Section 2.2.5. The animal types with specific
2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.1. Types of Animal Operations Covered by CAFO Regulations

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NPDES Permit Writers’ Manual for CAFOs

threshold numbers for the Large and Medium size categories identified in the regulations are
cattle, dairy cows, veal calves, swine, chickens, turkeys, ducks, horses, and sheep. Chapter 4 of the
Technical Development Document for the 2003 CAFO rule provides descriptions of those animal
types and their associated operations. An AFO that meets the small or medium size thresholds
can be designated as a CAFO by the permitting authority if certain criteria are met, including that
the AFO is determined to be “a significant contributor of pollutants to waters of the United States.”
40 CFR § 122.23(c). For further discussion, see Section 2.2.8.

2.2.2. Animal Types Not Listed in CAFO Regulations
An operation confining any animal type (e.g., geese, emus, ostriches, bison, mink, alligators)
not explicitly mentioned in the NPDES regulations and for which there are no ELGs is subject to
NPDES permitting requirements for CAFOs if (1) it meets the definition of an AFO, and (2) if the
permitting authority designates it as a CAFO. For a discussion of designation, see Section 2.2.8.

2.2.3. AFOs Defined as Large CAFOs
An AFO is a Large CAFO if it stables or confines equal to or more than the number of animals
specified in Table 2-1 for 45 days or more in a 12-month period. The definition of a Large CAFO is
based solely on the number of animals confined.
Table 2-1. Large CAFOs
Number of
animals
700

Type of animal
Mature dairy cows, whether milked or dry

1,000

Veal calves

1,000

Cattle, other than mature dairy cows or veal calves (Cattle includes but is not
limited to heifers, steers, bulls and cow/calf pairs.)

2,500

Swine, each weighing 55 pounds or more

10,000

Swine, each weighing less than 55 pounds

500

Horses

10,000

Sheep or lambs

55,000

Turkeys

30,000

Laying hens or broilers, if the AFO uses a liquid-manure handling system

125,000

Chickens (other than laying hens), if the AFO uses other than a liquid-manure
handling system

82,000

Laying hens, if the AFO uses other than a liquid-manure handling system

30,000

Ducks, if the AFO uses other than a liquid-manure handling system

5,000

Ducks, if the AFO uses a liquid-manure handling system

Source: 40 CFR § 122.23(b)(4)
2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.3. AFOs Defined as Large CAFOs

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In determining whether the applicable Large CAFO threshold is satisfied, the number of animals
actually maintained is considered, not the capacity of the operation.

Is this operation a Large CAFO?
Example A: An operation confines 2,800 mature swine (more than 55 pounds each) in six
houses. The houses have concrete floors with conveyances to capture manure.
Answer: The operation meets the definition of an AFO; it confines animals for more than
45 days over a 12-month period and the confinement area does not sustain vegetation. The
operation is a Large CAFO because it confines more than 2,500 mature swine, a number
that exceeds the regulatory threshold for a Large CAFO.
Example B: A 1,000-head cow/calf operation evenly splits its calving between fall and spring.
The animals are generally pastured with the exception of two 60-day periods when the cow/
calf pairs are confined for weaning. Because the calving is split, only 500 cow/calves are
confined in any one weaning session.
Answer: The operation meets the definition of an AFO because animals are confined for
45 days in a 12-month period. Because the operation does not confine 1,000 or more
animals or cow/calf pairs for more than 45 days, the operation is not defined as a Large
CAFO. The operation could be a Medium CAFO if it meets one of the two discharge criteria
for the Medium CAFO category, or is designated as a CAFO by the permitting authority.
Example C: A background yard (raises feeder cattle from the time calves are weaned until
they are on a finishing ration in the feedlot) has the capacity to hold 1,100 head of cattle. The
facility operates year-round (animals are confined 365 days a year) and has never confined
more than 800 head at any time.
Answer: The operation meets the definition of an AFO because animals are confined for
45 days in a 12-month period on a feedlot where vegetation is not sustained. Because the
operation does not confine 1,000 or more animals at any one time, the operation is not
defined as a Large CAFO. The operation could be a Medium CAFO if it meets one of the
two discharge criteria for the Medium CAFO category, or is designated as a CAFO by the
permitting authority.

2.2.4. Practices Constituting Poultry Operation Liquid-Manure
Handling
The thresholds for chicken and duck AFOs in the CAFO definitions are based on the type of
litter or manure handling system being used. The two systems are either a liquid-manure
handling system or other-than-a-liquid-manure handling system. The animal number thresholds
that determine whether the system is a CAFO for chicken or duck AFO using a liquid-manure
handling system are lower than the thresholds for CAFOs that use other-than-liquid-manure
handling systems.

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.4. Practices Constituting Poultry Operation Liquid-Manure Handling

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NPDES Permit Writers’ Manual for CAFOs

An AFO is considered to have a liquid-manure handling system if it uses pits, lagoons, flush
systems (usually combined with lagoons), or holding ponds, or has systems such as continuous
overflow watering, where the water comes into contact with manure and litter. In addition,
operations that stack or pile manure in areas exposed to precipitation are considered to
have liquid-manure handling systems. That includes operations that remove litter from the
confinement area and stockpile or store it uncovered in remote locations for even one day.
However, permitting authorities may authorize some limited period of temporary storage of litter
of no more than 15 days that would not result in the facility meeting the definition of a liquidmanure handling system (e.g., where time is needed to allow for contract hauling arrangements
and precipitation does not occur) (USEPA 2003, 3-6). If litter is stockpiled beyond that temporary
period, the uncovered stockpile would constitute a liquid-manure handling system, and the lower
CAFO thresholds for chickens and ducks would apply (see Tables 2-1 and 2-2).

Wet Lot and Dry Lot Duck Operations
Duck operations are considered to use a liquid-manure handling system if (1) the ducks are
raised outside with swimming areas or ponds or with a stream running through an open lot, or
(2) the ducks are raised in confinement buildings where fresh or recycled water is used to flush
the manure to a lagoon, pond, or other storage structure. In addition, a duck operation that stacks
manure or litter as described above for other dry poultry operations is considered to have a liquidmanure handling system.
Dry-lot duck operations include those that (1) use confinement buildings and handle manure and
litter exclusively as dry material; (2) use a building with a mesh or slatted floor over a concrete pit
from which manure is scraped into a solid manure storage structure; or (3) use dry bedding on a
solid floor. Dry-lot duck operations are generally considered to be “operations that use other than
a liquid-manure handling system.”

2.2.5. AFOs that Are Medium CAFOs
An AFO is a Medium CAFO if it meets both parts of a two-part definition. The first part addresses
the number of animals confined, and the second part includes specific discharge criteria. In
addition, a medium-sized AFO can be designated a CAFO by the permitting authority or EPA
(see Section 2.2.8). Table 2-2 lists the animal number ranges associated with the Medium CAFO
definition. If an AFO confines the number of animals listed in Table 2-2 for 45 days or more in a
12-month period, it meets the first part of the definition of a Medium CAFO.
An AFO meets the discharge criteria for the second part of the Medium CAFO definition if
pollutants are discharged in one of the following ways:
▶ Into waters of the U.S. through a man-made ditch, flushing system, or other similar
man-made device.

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.5. AFOs that Are Medium CAFOs

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▶ Directly into waters of the U.S. that originate outside the facility and pass over, across, or
through the facility or otherwise come into direct contact with the confined animals.
40 CFR § 122.23(b)(6).
Table 2-2. Medium CAFOs
Number of
animals

Type of animal

200–699

Mature dairy cows, whether milked or dry

300–999

Veal calves

300–999

Cattle, other than mature dairy cows or veal calves (Cattle includes but is not
limited to heifers, steers, bulls and cow/calf pairs.)

750–2,499
3,000–9,999
150–499
3,000–9,999
16,500–54,999
9,000–29,999

Swine, each weighing 55 pounds or more
Swine, each weighing less than 55 pounds
Horses
Sheep or lambs
Turkeys
Laying hens or broilers, if the AFO uses a liquid-manure handling system

37,500–124,999

Chickens (other than laying hens), if the AFO uses other than a liquid-manure
handling system

25,000–81,999

Laying hens, if the AFO uses other than a liquid-manure handling system

10,000–29,999

Ducks, if the AFO uses other than a liquid-manure handling system

1,500–4,999

Ducks, if the AFO uses a liquid-manure handling system

Source: 40 CFR § 122.23(b)(6)

The term man-made device means a conveyance constructed or caused by humans that
transports wastes (manure, litter, or process wastewater) to waters of the U.S. (USEPA 1995, 8).
Man-made devices include, for example, pipes, ditches, and channels. If human action was
involved in creating the conveyance, it is man-made even if natural materials were used to form
it. A man-made channel or ditch that was not created specifically to carry animal wastes but
nonetheless does so is considered a man-made device. To be defined as a Medium CAFO, there
must be an actual discharge of pollutants to waters of the U.S. However, it is not necessary for
the man-made device to extend the entire distance to waters of the U.S. It is sufficient that the
wastes being discharged flow through the man-made device. For example, a culvert could simply
facilitate the flow of waste¬water from one side of a road to another (and subsequently into a
water of the U.S.) and is a man-made device for the purposes of this provision. Also, a flushing
system is a man-made device that uses fresh or recycled water to move manure from the point of
deposition or collection to another location.

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.5. AFOs that Are Medium CAFOs

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Definition of Production Area
Production area means that part of an AFO that includes the animal confinement area, the manure
storage area, the raw materials storage area, and the waste containment areas. The animal confinement area includes but is not limited to open lots, housed lots, feedlots, confinement houses, stall
barns, free stall barns, milkrooms, milking centers, cow yards, barnyards, medication pens, walkers,
animal walkways, and stables. The manure storage area includes but is not limited to lagoons, runoff ponds, storage sheds, stockpiles, under house or pit storages, liquid impoundments, static piles,
and composting piles. The raw materials storage area includes but is not limited to feed silos, silage
bunkers, and bedding materials. The waste containment area includes but is not limited to settling
basins, and areas within berms and diversions, which separate uncontaminated stormwater. Also
included in the definition of production area is any egg-washing or egg-processing facility, and any
area used in the storage, handling, treatment, or disposal of mortalities.
40 CFR § 122.23(b)(8)

Tile drains in the production area are another example of a man-made device. Tile drains are
underground pipes that collect subsurface water for transport away from the site. If tile drains
discharge manure to waters of the U.S. from the production area of a medium-sized AFO, the
facility meets discharge criterion for the Medium CAFO definition and is a Medium CAFO. An
additional example would be the discharge to waters of the U.S. from a continuous-flow-through
water trough system.
The Medium CAFO definition addresses discharges directly into a water of the U.S., which
originate outside the facility and pass over, across, or through the facility or otherwise come
into direct contact with the confined animals. The discharge criterion is met if animals in
confinement at an AFO can come into direct contact with waters of the U.S. Thus, a stream
running through the area where animals are confined indicates that there is a direct discharge of
pollutants unless animals are prevented from any direct contact with waters of the U.S.

Is this operation a Medium CAFO?
Example A: Runoff from an earthen lot with 850 beef cattle, confined for 6 months a year,
passes through a settling basin, riser pipe, concrete channel, junction box, and distribution
manifold before flowing by gravity to an area where it infiltrates into the soil and does not
reach waters of the U.S.
Answer: No. While the system described includes several man-made devices, the operation
does not meet the definition of a Medium CAFO because the runoff does not enter waters of
the U.S.
Example B: A 400-head beef cattle AFO, operated year-round, has a grassed waterway
installed adjacent to the production area that transports contaminated runoff to an open field.
There is no surface water in the area where the runoff is transported.
Answer: No. While a properly designed grassed waterway is a man-made device, the
discharge does not reach a water of the U.S. If the discharge reached a water of the U.S.,
the facility would be a CAFO.

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.5. AFOs that Are Medium CAFOs

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2.2.6. Operations under Common Ownership
Under the CAFO regulations, two or more AFOs under common ownership are considered one
operation if, among other things, they adjoin each other (including facilities that are separated
only by a right-of-way or a public road) or if they use a common area or system for managing
wastes. 40 CFR § 122.23(b)(2). For example, operations generally meet the criterion where
manure, litter, or process wastewater are commingled (e.g., stored in the same pond, lagoon, or
pile) or are applied to the same cropland.
In determining whether two or more AFOs are under common ownership, the number of
managers is not important. Two AFOs could be managed by different people but have a common
owner (e.g., the same family or business entity owns both). For facilities under common
ownership that either adjoin each other or use a common area or system for waste disposal, the
cumulative number of animals confined is used to determine if the combined operation is a Large
CAFO and is used in conjunction with the discharge criteria in Section 2.2.5 to determine if the
combined operation is a Medium CAFO.

Is this operation under Common Ownership?
Example: If a single farm has six chicken houses with a total of 125,000 birds, and the houses
are managed by two people, is the farm considered a CAFO?
Answer: Yes. The chicken houses are part of a single operation and presumably use a
common area or system for the disposal of wastes; therefore, the entire operation is a Large
CAFO. The number of managers is not relevant.

2.2.7. Operations with Multiple Animal Types
Under the CAFO regulations, multiple types of animals are not counted together to determine
the type and size of a CAFO. However, once an operation is defined as a CAFO on the basis of a
single animal type, all the manure generated by all animals confined at the operation are subject
to NPDES requirements. If wastestreams from multiple livestock species subject to different
regulatory requirements are commingled at a CAFO, any NPDES permit for the facility must
include the more stringent ELG requirements. 2003 CAFO Rule, 68 FR 7176, 7,195 (Feb. 12, 2003).
See Appendix N, References for NPDES Permit Writers.
In situations where immature animals (e.g., heifers and swine weighing less than 55 lbs) are
confined along with mature animals, the determination of whether the operation is defined as
a CAFO depends on whether the mature or immature animals separately meet the applicable
threshold. Operations that specialize in raising only immature animals (heifers, swine weighing
less than 55 lbs, and veal calves) have specific thresholds under the regulations. However, once
an AFO is defined as a CAFO, manure generated by all the animals in confinement would be
addressed by the CAFO’s NPDES permit if it is a permitted CAFO.
2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.7. Operations with Multiple Animal Types

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Is this AFO a CAFO?
Example A: A dairy operation confines year-round 275 dry mature dairy cows, 500 lactating
mature dairy cows, and 800 heifers.
Answer: The operation meets the definition of a Large CAFO because it confines more
than 700 (in this case 775) mature dairy cows, milked or dry for more than 45 days. The
800 heifers alone would not meet the threshold for a Large CAFO. If the CAFO obtains
permit coverage, the manure from all the animals confined, including the heifers, would be
subject to the ELG and would need to be addressed in the CAFO’s NMP.
Example B: A swine nursery operation has 15,000 piglets that range in weight from 40 to
60 pounds. The operation also has a farrowing house with 2,200 sows and approximately
13,000 piglets that are not weaned. The operation maintains that number of animals yearround.
Answer: The operation would meet the definition of a Large CAFO if it has at least
10,000 piglets that weigh under 55 pounds confined for more than 45 days. If the CAFO
obtains permit coverage, the manure from all the animals confined would be subject to the
ELG and would need to be addressed in the CAFO’s NMP.
Example C: An operation confines for more than 45 days 250 beef cattle, 20 horses, and
22,000 chickens (does not use a liquid-manure handling system).
Answer: The operation does not meet the definition of a CAFO. The number of animals of
any one animal type that are confined for 45 days in a 12-month period does not exceed
the thresholds for a Large or Medium CAFO. Because sufficient animals are not confined,
there is no need to determine whether the AFO meets one of the two discharges criteria to
be defined as Medium CAFO. However, the operation could still be designated as a CAFO
if the appropriate authority determines that the operation is a significant contributor of
pollutants to waters of the U.S.

An operation that confines multiple animals types, where no one type meets the Large
or Medium CAFO threshold, can be designated as a CAFO if it is found to be a significant
contributor of pollutants to waters of the U.S. For additional discussion of designated CAFOs, see
Section 2.2.8.

2.2.8. AFOs Designated as CAFOs
The CAFO regulations set the standards for the Director (either the Regional Administrator or
the NPDES permitting authority) to designate any AFO as a CAFO if the AFO is a significant
contributor of pollutants to waters of the U.S.1 Designation provides for protection of surface water
quality while maintaining flexibility for states or other entities to assist small and medium AFOs
to mitigate the conditions that could subject the AFO to NPDES requirements.2

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.8. AFOs Designated as CAFOs

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The Director may designate any AFO as a CAFO on a case-by-case basis if he determines
that the AFO is a significant contributor of pollutants to waters of the U.S. as specified in
40 CFR part 122.23(c). AFO operations that may be considered for designation include the
following:
▶ A medium-sized AFO that is not defined as a CAFO and is determined to be a
significant contributor of pollutants to waters of the U.S. The definition of a Medium
CAFO is in the text box provided.
▶ A small AFO (i.e., confines fewer than the number of animals defined in Table 2-2) that
meets one of the methods of discharge criteria in 40 CFR sections 122.23(c)(3)(i), (ii)
and is determined to be a significant contributor of pollutants to waters of the U.S.
▶ An AFO that raises animals other than species identified in the regulatory definitions
of Large and Medium CAFOs and is determined to be a significant contributor of
pollutants to waters of the U.S. Examples of such AFOs include geese, emus, ostriches,
llamas, minks, bison, and alligators.

Medium CAFO Definition Discharge
• Pollutants are discharged into waters of the U.S. through a man-made ditch,
flushing system, or other similar man-made device; or
• Pollutants are discharged directly into waters of the U.S. that originate
outside and pass over, across, or through the facility or otherwise come into
direct contact with animals confined in the operation.
40 CFR §§ 122.23(b)(6)(ii)(A), (B)

2.2.9. Process for Designating an AFO as a CAFO
For an AFO to be designated as a CAFO, the Director must determine that the AFO is a significant
contributor of pollutants to waters of the U.S. 40 CFR part 122.23(c). Once an operation is
designated as a CAFO, it must seek coverage under an NPDES permit and, among other things,
develop and implement an NMP.
Under 40 CFR part 122.23(c)(3), an AFO may not be designated as a CAFO until the NPDES
permitting authority or EPA has determined that the operation should and could be regulated
under the permit program and conducted an inspection of the operation. In addition, a small
AFO may not be designated as a CAFO unless it also meets the small AFO discharge criteria,
40 CFR parts 122.23(c)(3)(i), (ii), and is determined to be a significant contributor of pollutants to
waters of the U.S. EPA recommends that the designation process be conducted as soon as possible
following the inspection. Regardless of when an inspection takes place, the designation should be
based on current information.

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.9. Process for Designating an AFO as a CAFO

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In determining whether an AFO is a significant contributor of pollutants to waters of the U.S., the
permitting authority or EPA Regional Administrator (see Section 2.2.10) will consider the factors
specified in 40 CFR part 122.23(c)(2), which are listed in the left-hand column of Table 2-3, below.
The right-hand column in Table 2-3 gives examples of case-by-case designation factors that can
be assessed during the designation inspection. The assessment of regulatory factors may be based
on visual observations and water quality monitoring and other sources of relevant information.
Table 2-3. Example factors for case-by-case CAFO designation
Designation factor

Example factors for inspection focus

Size of the operation and
amount of wastes reaching
waters of the U.S.

• Number of animals
• Type of feedlot surface
• Feedlot design capacity
• Waste handling/storage system design capacity

Location of the operation
relative to waters of
the U.S.

• Location of waterbodies
• Location of floodplain
• Proximity of production area and land application area to waters
of the U.S.
• Depth to groundwater, direct hydrologic connection to waters
of the U.S.
• Located in an impaired watershed

Means of conveyance of
animal wastes and process
wastewaters into waters of
the U.S.

• Identify existing or potential man-made (includes natural and
artificial materials) structures that could convey waste

Slope, vegetation, rainfall,
and other factors affecting
the likelihood or frequency
of discharge of manure
into waters of the U.S.

• Slope of feedlot and surrounding land

• Direct contact between animals and waters of the U.S.

• Type of feedlot (concrete, soil)
• Climate (e.g., arid or wet)
• Type and condition of soils (e.g., sand, karst)
• Drainage controls
• Storage structures
• Amount of rainfall
• Volume and quantity of runoff
• High water table
• Buffers

Other relevant factors

• History of noncompliance
• Use of conservation practices to minimize nutrient transport to
waters of the U.S.
• Working with USDA or Soil and Water Conservation District to
improve operation

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.9. Process for Designating an AFO as a CAFO

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NPDES Permit Writers’ Manual for CAFOs

Following the on-site inspection for designation, the NPDES permitting authority should prepare
a brief report that (1) identifies findings and any follow-up actions, (2) determines whether the
facility should or should not be designated as a CAFO, and (3) documents the reasons for that
determination. Regardless of the outcome, the permitting authority should prepare a letter to
inform the facility of the results of the inspection and, if appropriate, propose that the facility
be designated as a CAFO. The letter should explain that EPA regulations would require the
operation to seek coverage under an NPDES permit if it is designated. After providing the CAFO a
reasonable opportunity to respond with any questions or concerns, the permitting authority may
then send the CAFO a final designation letter. The letter should indicate whether a general permit
is available or whether an individual permit application should be submitted by a specific date.
In those cases where a facility has not been designated as a CAFO but the NPDES permitting
authority has identified areas of concern, the authority should note those areas in the letter. The
letter should state that if the concerns are not corrected, the facility could be designated as a
CAFO in the future. The letter should also include a date for a follow-up inspection to determine
whether the concerns have been adequately addressed. Samples of letters that would be used
at the conclusion of a designation inspection are in Appendix B, Example Letters to Owners/
Operators after a Site Visit.
The following are examples of situations that might warrant CAFO designation.
▶ An AFO that maintains 350 cattle is adjacent to a river that is impaired as a result of
nutrient loading. The operator routinely piles the waste next to the enclosure where
it remains until a contract hauler picks it up. The waste is removed monthly, but
precipitation occurs several times a month; runoff from the stockpiled manure flows
through naturally occurring channels in the ground to the river. The facility would be
a candidate for inspection and designation as a CAFO (the permitting authority also
could recommend site modification). Note that an AFO that confines the number of
animals specified in 40 CFR part 122.23(b)(6) (Medium CAFO) does not need to meet
the discharge criteria specified in parts 122.23(c)(3)(i) or (ii) to be designated as a
CAFO. For a discussion of Medium CAFOs, see Section 2.2.5.
▶ An AFO with 650 swine is crossed by a stream that originates outside the facility. The
stream flows through an open lot where the animals are confined and continues on
to connect with other waters of the U.S. beyond the facility. The facility would be a
candidate for inspection and designation as a CAFO. Because the facility is a small
AFO, meeting one of the discharge criteria in 40 CFR parts 122.23(c)(3)(i) or (ii) is a
necessary condition for designation.

2.2.10. EPA Designation in NPDES Authorized States
The CAFO regulations authorize the EPA Regional Administrator to designate AFOs as CAFOs
in NPDES-authorized states and tribal areas where the Regional Administrator has determined
that one or more pollutants in an AFO’s discharge contribute to an impairment in a downstream
or adjacent state or Indian country water that is impaired for that pollutant or pollutants.
2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.10. EPA Designation in NPDES Authorized States

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Such designation is based on assessment of the factors in §122.23(c)(2) and requires an on-site
inspection. Upon designation by EPA, the operation would be required to apply to the permitting
authority for permit coverage. EPA designation in NPDES-authorized states is intended to ensure
consistent implementation of designation requirements across state or tribal boundaries where
serious water quality concerns exist. If EPA decides that the AFO does not need to be designated
as a CAFO, EPA may work with the state permitting authority to identify other appropriate
actions.

References
USEPA (U.S. Environmental Protection Agency). 1995. Guide Manual on NPDES Regulations for
Concentrated Animal Feeding Operations. EPA-833-B-95-001. U.S. Environmental Protection
Agency, Office of Water, Washington, DC.
USEPA (U.S. Environmental Protection Agency). 2002. Development Document for the Final
Revisions to the National Pollutant Discharge Elimination System Regulation and the Effluent
Guidelines for Concentrated Animal Feeding Operation. EPA-821-R-03-001. U.S. Environmental
Protection Agency, Washington, DC.
USEPA (U.S. Environmental Protection Agency). 2003. NPDES Permit Writers’ Guidance Manual
and Example Permit for Concentrated Animal Feeding Operations. EPA-833-B-04-001.
U.S. Environmental Protection Agency, Washington, DC.

Endnotes
40 CFR part 122.23(c); for more information about EPA designation in authorized states, see Section 2.2.10.

1

The Manual does not address how the CWA applies to discharges from AFOs that are not defined or designated as
CAFOs.

2

2. AFOs and CAFOs
2.1. Animal Feeding Operations (AFOs)

2.2. Concentrated Animal Feeding Operations (CAFOs)
2.2.10. EPA Designation in NPDES Authorized States

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Chapter

3

3. Appropriate Permitting
Strategies for CAFOs
NPDES permitting authorities have two options for issuing NPDES permits to CAFOs: individual
permits and general permits. This chapter describes the administrative process for both
permitting options and situations in which one or the other might be more appropriate.

3.1. NPDES CAFO Permit Applications and Notice of
Intent
CAFO owners and operators who are required to seek permit coverage must either submit
an application for an individual permit or submit a Notice of Intent (NOI) (or permitting
authority’s comparable form) for coverage under a general permit, if a general permit is available.
40 CFR § 122.23(d)(1).
The 2008 CAFO regulations amend the information requirements for seeking coverage under
an NPDES permit for CAFOs. The regulations revised the NPDES individual permit application
and general permit NOI form for CAFOs (Form 2B); specifically, the information required to be
submitted for coverage under either type of CAFO permit. 40 CFR §§ 122.21(i)(1), 122.23(h). The
permitting authority can use Form 2B for both NPDES CAFO permit applications and NOIs. The
NOI/Permit Application for CAFOs is located at http://www.epa.gov/npdes/pubs/cafo_fedregstr_
form2b.pdf. EPA requires applicants who seek coverage under either individual or general CAFO
permits to provide, at a minimum, the information listed in Table 3-1.
To the extent that a permitting authority needs additional information to review a permit
application, the NPDES permitting authority may request additional information from the
applicant and use other Clean Water Act (CWA) information-gathering authorities, such as
CWA part 308, to obtain such information.

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Table 3-1. Information required on NPDES application forms 1 and 2B
Form 1 (all
NPDES individual
permit applicants)
40 CFR § 122.21 (f)

Activities conducted by the applicant that require an NPDES permit
Name, mailing address, and location of facility
Up to four Standard Industrial Classification codes that best reflect the
principal products or services provided
Operator’s name, address, and telephone number and ownership status
Whether the facility is on Indian lands
List of all other state or federal permits or construction approvals received or
applied for under CWA, Resource Conservation and Recovery Act (RCRA), Safe
Drinking Water Act (SDWA), etc.
Brief description of the nature of the business

Form 2B (CAFOs)
40 CFR § 122.21 (i)

The name, address, and telephone number of the owner or operator
Whether the application is for an existing or proposed facility
Facility name, address, and telephone number
Latitude and longitude of the production area
Name and address of integrator for contract operations
Specific information about the number and type of animals, whether in open
confinement or housed under roof
Total number of acres under control of the applicant available for land
application of manure, litter, or process wastewater
Estimated amounts of manure, litter, and process wastewater generated per
year
Estimated amounts of manure, litter, and process wastewater transferred to
other persons per year
Topographic map of the geographic area in which the CAFO is located
showing the specific location of the production area
Containment and storage type and storage capacity for manure, litter, and
process wastewater
A nutrient management plan that satisfies the requirements specified in
40 CFR part 122.42(e), including, for all CAFOs subject to 40 CFR part 412,
subpart C or subpart B, the requirements of 40 CFR part 412.4(c), as
applicable
Indication of whether a nutrient management plan is being implemented
Date of last nutrient management plan review or revision
Description of alternative uses of manure, litter, and process wastewater
Identification of land application best management practices implemented

3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage

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NPDES Permit Writers’ Manual for CAFOs

3.1.1. CAFO Permit Application or Notice of Intent
Requirements for Nutrient Management Plans
Any CAFO seeking NPDES permit coverage must submit an NMP as part of its permit
application to be covered by an individual permit or an NOI to be covered by a general permit.
40 CFR §§ 122.23(h), 122.42(e)(1). The NMP must meet the requirements of 40 CFR part 122.42(e).
NMPs for Large CAFOs subject to subparts C or D of 40 CFR part 412 must also meet the require­
ments of part 412.4(c), as applicable. 40 CFR §§ 122.21(i)(1)(x), 122.23(h). EPA’s application Form 2B
reflects those changes. The NOI/Permit Application for CAFOs is located at http://www.epa.gov/
npdes/pubs/cafo_fedregstr_form2b.pdf.
An NMP is a manure and wastewater management tool that every permitted CAFO must use to
properly manage discharges from the production or land application areas. The requirements for
an NMP are discussed in Section 4.1.7 and Chapters 5 and 6 of this Manual.

3.2. Individual NPDES Permits for CAFOs
An individual permit is a permit specifically tailored for an individual facility. Upon receiving a
permit application from a facility seeking permit coverage, the permitting authority must make
a determination whether to issue a permit or request additional information from the facility
seeking permit coverage. After determining that a facility is eligible for permit coverage, the
permitting authority develops a permit for the facility on the basis of the information in the
permit application (e.g., type of activity, nature of discharge, receiving water quality). Following
notice and the opportunity for public comment, the permit is then issued to the facility for a
specific period (not to exceed 5 years) with a requirement to reapply before the expiration date.
The permitting authority may decide to use individual permits for some of or all the CAFOs
within the jurisdiction of the permitting authority. Those include circumstances in which
the permitting authority prefers, for administrative reasons, to use individual permits for
all permitted CAFOs and situations in which an individual permit is the appropriate permit
mechanism for a facility.
Following are reasons why a permitting authority might use individual permits for all permitted
CAFOs:
▶ A small number of CAFOs are in the permitting authority’s jurisdiction.
▶ Historical use of individual CAFO permits by the permitting authority.
▶ Preference to stagger review of site-specific information in determining appropriate
permit conditions.

3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage

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Alternatively, a permitting authority may elect to use a general permit for some CAFOs and
individual permits for other CAFOs. For example, the permitting authority might prefer to use
an individual permit for a CAFO that presents unique circumstances best addressed through the
individual permitting process, or the permitting authority may require a CAFO that discharges,
but is not eligible for coverage under a general permit, to apply for and obtain an individual
NPDES permit. In addition, the permitting authority may require any CAFO authorized by a
general permit to apply for coverage under an individual NPDES permit. 40 CFR §§ 122.23(h)(3),
(b)(3). Further, any interested person may petition the permitting authority to require a CAFO to
apply for coverage under an individual permit. 40 CFR § 122.28(b)(3).
Whether a CAFO should be required to obtain an individual NPDES permit, even where the
CAFO might be eligible for or covered by a general permit, is a determination that remains within
the discretion of the permitting authority. 40 CFR § 122.28(b)(3). In making such a determination,
the permitting authority might wish to consider the following factors, such as whether the CAFO
▶ Is exceptionally large (existing and new operations).
▶ Has historical compliance problems.
▶ Has significant site-specific environmental concerns (e.g., proximity to a water of the
U.S., discharges of stormwater from outside the production area, or other discharges
that are not specifically addressed by the general permit).
▶ Is in an area of significant environmental concern or with particular water quality
impairment (may also be addressed in a watershed permit).

Individual permits may be appropriate for CAFOs that have significant site-specific
environmental concerns (e.g., proximity to a water of the U.S., discharges of stormwater
from outside the production area, or other discharges that are not specifically addressed by
the general permit). (Source: New Mexico Environment Department (left);
USDA/NRCS (right))

3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage

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NPDES Permit Writers’ Manual for CAFOs

▶ Is subject to voluntary alternative
performance standards for the
production area (see Appendix F,
Voluntary Alternative Performance
Standards for CAFOs).
▶ Is subject to additional state
requirements that apply to specific
areas or operations (may also be
addressed in a watershed permit).
▶ Have operations subject to
other NPDES permits (e.g.,
slaughterhouses, ethanol plants),
the complexity of which warrants
consolidation of multiple types of
permit conditions into a single,
comprehensive, individual permit.

Proximity of production areas to waters of the U.S. is a
consideration for requiring an individual permit.
(Photo courtesy of USDA/NRCS)

3.2.1. Developing Individual NPDES Permits for CAFOs
An individual NPDES permit for a CAFO is developed in the same manner as an NPDES permit
for a facility in any other sector. After receiving the permit application, the permit writer develops
a draft permit and fact sheet for a facility on the basis of the information in the facility’s submitted
application.1 In addition, where facility inspection report(s) are available to the permitting
authority, they may be used to supplement the development of permit conditions. Appendix N,
References for NPDES Permit Writers, contains a list of possible references for the permit writer in
support of NPDES permit development.
The permit application (including the facilityspecific NMP), draft permit, and fact sheet
must be made available for public review
and comment. 40 CFR § 124.10(d)(iv). EPA
expects that the additional information in
the application and public notice together
will provide the public with a meaningful
opportunity to review the CAFO’s NMP
and the detailed requirements of the draft
permit, including the terms of the NMP to
be included in the permit, and provide the
public with the opportunity to comment
on the adequacy of both the NMP and the
terms and conditions of the permit. After
reviewing the draft permit and the permit

A location with historical compliance problems may need an
individual permit. (Photo courtesy of USDA/NRCS)

3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.2.1. Developing Individual NPDES Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage

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NPDES Permit Writers’ Manual for CAFOs

application, including the facility-specific
NMP, and any other documentation requested
by the permitting authority (e.g., plans and
specifications for waste storage structures), the
public would have an opportunity to seek more
information, to raise concerns, or to request
a hearing. The public notification and review
process is discussed in more detail below in
Section 3.4.
Water quality-based effluent requirements
must also be included in permits where
technology-based requirements are not
sufficient to ensure compliance with state
water quality standards or where required
An individual permit can be used for facilities subject to
to implement a Total Maximum Daily
voluntary alternative performance standards, such as this
Load (TMDL). If water quality concerns are
CAFO with a settling basin and filter strip.
(Photo courtesy of USDA/NRCS)
associated with discharges from a CAFO
seeking coverage under an individual NPDES
permit, the permitting authority should take special steps to ensure that it has the necessary
information needed to prepare the draft permit and fact sheet. Such information might include
information on receiving water impairments, ambient water quality data, TMDL wasteload
allocations, or facility-specific discharge data, design specifications, or operational plans. The
permitting authority may use its CWA section 308 authority or corresponding state authorities
to obtain additional information or conduct a site inspection while developing the draft permit.
For CAFOs that are covered under an existing NPDES permit, the standard permit condition
for Inspection and Entry, at 40 CFR part 122.41(i) also provides authority to obtain additional
information or conduct a site visit to support draft permit development.

3.3. NPDES General Permits for CAFOs
An NPDES general permit covers a category of point sources with similar characteristics for a
specific geographic area (e.g., watershed, county, region, state). The scope of the permit may
include all CAFOs in a geographic area, or it may be limited to particular animal sectors or
sizes of operations. CAFOs may appropriately be covered under an NPDES general permit
because CAFOs generally involve similar types of operations, require the same kinds of effluent
limitations, permit conditions, and discharge the same types of pollutants. As discussed in
Section 3.2 above, there are circumstances where an individual NPDES permit might be more
appropriate for a CAFO even though a general permit is available.
General permits offer a cost-effective approach for NPDES permitting authorities because they
can cover a large number of facilities under one permit. CAFO general permits can be developed
to cover one or several animal livestock sectors. EPA anticipates that states will use various
3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage

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NPDES Permit Writers’ Manual for CAFOs

approaches for establishing their NPDES general
CAFO permit program. In some cases, a single
general permit covering all the CAFOs in a state
might be appropriate. In other situations, a specific
permit for each animal sector might be the best
approach. States may also elect to issue different
general permits for existing and new sources.
NPDES general permits should contain special
provisions that identify facilities that are more
appropri­ately covered under individual NPDES
permits (see Section 3.2). For example, states may
develop their NPDES general permits in a way that
limits coverage to facilities of a certain size, thereby
requiring CAFOs above a certain threshold to apply
for an individual NPDES permit. Alternatively, states
may choose to develop their NPDES general permits
so that they identify certain facilities as a separate
class of CAFOs (e.g., very large, impaired waters)
that need to meet additional permit conditions
identified in the general permit. The sample permit
in Appendix J, NPDES General Permit Template for
CAFOs, of this Manual has been set up to address all
existing CAFOs that are subject to subparts C and D
of the ELG.

States may require additional practices
such as terraces, conservation tillage,
and conservation buffers for CAFOs in
environmentally sensitive areas.
(Photo courtesy of USDA/NRCS)

3.3.1. Developing NPDES General Permit for CAFOs
The CAFO regulations include unique requirements that must be met when issuing a general
permit for CAFOs. 40 CFR § 122.23(h). NPDES general permits for CAFOs are required to be
developed and issued through a two-stage process. 40 CFR § 122.23(h). Permit requirements
applicable to all permittees are developed in the first stage, following the requirements of
40 CFR part 122.28. In the second stage, following submission of a CAFO’s NOI and NMP, the
permitting authority must include additional, site-specific requirements in the general permit
pursuant to the requirements of 40 CFR part 122.23(h).
In developing and issuing an NPDES general permit, following the procedural requirements of
40 CFR part 122.28, the NPDES permitting authority develops a draft permit and a fact sheet that
defines the following: the scope of the permit, the facilities that qualify for coverage under the
permit, and the specific terms and conditions that apply to the permittees. 40 CFR § 122.23(h).
The permitting authority must then make the draft permit and fact sheet available for review
through public notice and comment.
Given the significant public interest in animal waste management and CAFO permitting, EPA
strongly encourages effective public outreach when providing public notice of draft NPDES
3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage

3.3.1. Developing NPDES General Permit for CAFOs

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NPDES Permit Writers’ Manual for CAFOs

general permits for CAFOs. Permitting authorities are encouraged
to schedule public outreach meetings to explain permit
requirements and seek public input. After comments have been
considered and, when appropriate, a public hearing has been held,
the final permit is issued, usually for a 5-year term. That completes
the first stage of development of a general permit for CAFOs.

Some states have additional
requirements for certain types of
facilities, such as covering temporary
litter stockpiles at poultry operations.
(Source: Alabama Department of
Environmental Management.

To obtain coverage under a general permit, CAFO owners and
operators must submit an NOI to be covered by the permit. As with
other NPDES general permits, NPDES general permits for CAFOs
must specify the deadlines for submitting NOIs to be covered and
the date(s) when a permittee may be covered by the NPDES general
permit. 40 CFR § 122.28(b)(2).

A complete and timely NOI fulfills the requirements of a permit
application and indicates the owner or operator’s intent to abide by
all the conditions of the permit. The contents of the NOI must be clearly specified in the general
permit and must include, at a minimum, requirements specified in 40 CFR part 122.21(i)(1). The
information requirements for an NPDES CAFO general permit NOI and an NPDES CAFO individual permit application form are the same (see Table 3-1). The NOI/Permit Application for CAFOs is
located at http://www.epa.gov/npdes/pubs/cafo_fedregstr_form2b.pdf. The form contains the minimum federal requirements. Additional, state-specific requirements might need to be addressed.
An owner or operator of a CAFO eligible to seek coverage under an NPDES general permit may
request to be excluded from coverage under that general permit by applying for an NPDES
individual permit. 40 CFR § 122.28(b)(3)(iii). Consistent with provisions in the NPDES regulations
40 CFR part 122.28(b)(3), any interested party may petition the Director of the NPDES permitting
authority to require any specific facility to be covered under an individual permit.

Once an NOI (including a facility-specific NMP) is received by the permitting authority from a
CAFO seeking coverage under the general permit, the second stage of the NPDES general permitting process for CAFOs is initiated pursuant to 40 CFR part 122.23(h). The permitting authority
must notify the public as to which CAFOs are seeking coverage under the general permit before
cover­age takes effect for those facilities. After reviewing the NOI, including the facility-specific
NMP and any other documentation requested by the permitting authority (e.g., plans and
specifica­t ions for waste storage structures), as well as the draft terms of the NMP to be incorporated into the permit, the public has an opportunity to seek more information, raise concerns,
petition the permitting authority for individual permit coverage, or request a hearing concerning
CAFOs seeking coverage under the general permit. 40 CFR § 122.23(h). The process for the second
stage of the general permitting process for CAFOs is discussed in greater detail in Section 3.4.
Because the NOI also provides essential compliance information, the permitting authority
should ensure that the information is entered into EPA’s NPDES data system (either the Permit
Compliance System or the Integrated Compliance Information System).
3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage

3.3.1. Developing NPDES General Permit for CAFOs

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NPDES Permit Writers’ Manual for CAFOs

3.3.2. Watershed-Based NPDES Permits
Watershed-based permits are NPDES permits that are issued to point sources on a geographic
or watershed basis. They focus on watershed goals and consider the impact of multiple pollutant
sources and stressors, including those from nonpoint sources. A watershed approach provides
a framework for addressing all stressors in a hydrologically defined drainage basin instead of
viewing individual pollutant sources in isolation. More than 20 states have implemented some
form of the watershed approach and manage their resources on a rotating basin cycle. Because of
the recent emphasis on watershed-based permits and development of TMDLs that focus on water
quality impacts, EPA is looking at ways to use watershed-based permits to achieve watershed
goals. The watershed-based permit is a tool that can assist with implementing a watershed
approach. The utility of the tool relies heavily on a detailed, integrated, and inclusive watershed
planning process. That process and data needs for developing a watershed-based permit are
very similar to those needed for developing a TMDL and, therefore, they are most commonly
used in situations where there is a TMDL or similar watershed analysis that provides the basis
for permit requirements. For example, North Carolina’s nutrient management strategy for the
Neuse River Basin includes a watershed-based permit approach for TMDL implementation.
The strategy recognizes the need for all groups to work together and includes an approach for
permitted dischargers to work collectively to meet a combined nitrogen allocation, rather than
be subject to individual allocations. Connecticut followed a similar approach to permit publicly
owned treatment works discharging nutrients to Long Island Sound using a general permit that
addresses only nutrients to supplement the facilities’ individual permits.
A watershed-based permitting approach could be useful for CAFO permitting where a TMDL
or other watershed analysis for nutrients has been completed and CAFOs are identified as a
significant source of nutrients in the watershed. The TMDL or watershed analysis could allocate
nutrient loadings to CAFOs in the watershed as a category or as individual sources. For example,
to achieve the overall nutrient loading requirements for the watershed, CAFOs in an impaired
watershed might be required to implement enhanced management practices for land application
that are demonstrated to provide greater reduction of nutrient loadings than the requirements
imposed on CAFOs in a non-impaired watershed.
Where a permitting authority uses a watershed-based permitting approach, the permitting
authority might develop a set of individual permits and coordinate the timing of permit issuance
on a watershed basis. Alternatively, the permitting authority might issue a watershed-based
general permit that covers multiple sources (similar to the watershed-based permits in North
Carolina and Connecticut). If the permitting authority chooses to issue a general permit, the
permit must include provisions that specifically address the requirements applicable to CAFO
general permits set forth in 40 CFR part 122.23(h). The general permit can include requirements
that apply to all covered CAFOs and specific requirements that apply to individual CAFOs to
assure attainment of water quality standards.

3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.3.2. Watershed-Based NPDES Permits

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage

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NPDES Permit Writers’ Manual for CAFOs

3.4. Procedures for Permitting Authority Review and
Public Participation Before Permit Coverage
When a permitting authority receives an application or an NOI from a CAFO, it is the
permitting authority’s responsibility to review the application or NOI to ensure that it meets the
requirements of the regulations, and for general permits, the requirements set forth in the general
permit. 40 CFR § 122.23(h). In both instances, the permitting authority must determine whether
the NMP submitted by the CAFO meets the requirements in 40 CFR parts 122.21(f) and (i). As part
of that process, the permit writer must review the NMP for both completeness and sufficiency.
Also, because the terms of the NMP are to be incorporated as permit terms, the permitting
authority must provide for adequate public participation in the process of establishing permit
terms on the basis of each CAFO’s NMP. 40 CFR § 122.23(h).
As noted above, the general permit issuance process and the individual permitting process differ
in how a permit is developed and the means by which individual facilities obtain authorization to
discharge.

3.4.1. Individual Permit
For individual permits, the NMP will be submitted and reviewed as part of the permit
application. The decision-making procedures in 40 CFR part 124 apply to the Director’s review
of the application, which includes the NMP. Part 124 requires review of the completeness and
sufficiency of the permit application, including a requirement for the CAFO to modify the plan
or provide additional information to the permitting authority as necessary, and requires a final
decision by the Director after an opportunity for the public to comment and request a hearing.

3.4.2. General Permit
The 2008 CAFO regulations establishes public participation requirements that ensure adequate
opportunity for public review of both a CAFO’s NMP and the terms of the NMP to be incorporated
into the permit before any CAFO obtaining authorization to discharge under an NPDES general
permit. 40 CFR § 122.23. Thus, a second round of public notice and comment is necessary when
providing coverage for CAFOs under a general permit, and it is then that the public is provided
an opportunity to review the CAFO’s site-specific NMP and comment on terms of the NMP to be
incorporated into the permit. 40 CFR § 122.23(h).
As in the case of individual permit coverage, the Director must review the NOI submitted
by a CAFO owner or operator to ensure that the NOI includes the information required by
40 CFR part 122.21(i)(1), including an NMP that meets the requirements of 40 CFR part 122.42(e)
and applicable effluent limitations and standards, including those specified in 40 CFR part 412.
Part 122.23(h)(1) also provides that if, on review, the permitting authority determines that
additional information is necessary to complete the NOI or clarify, modify, or supplement
previously submitted material, the Director will notify the CAFO owner or operator and request
3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage
3.4.2. General Permit

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NPDES Permit Writers’ Manual for CAFOs

that the appropriate information be provided. When the NOI is complete, the Director must then
proceed with the public notification process required by the rule and discussed below.
To provide permitting authorities flexibility to review NMPs of varying complexity, there is no
specific time frame required for completion of the permitting authority review process. This
approach is consistent with the existing NPDES regulations in Part 124 for other industries, which
do not specify a time frame for automatic authorization to discharge or for the completion of the
permitting authority and public review processes.
The permitting authority is responsible for reviewing NMPs and for ensuring that the terms
of the NMP meet the applicable requirements of the NPDES process. There is no reason why a
state cannot obtain assistance and advice from technical experts such as state-certified nutrient
management planners. However, it is the permitting authority’s responsibility to ensure that
comments are properly addressed and the final permit terms are incorporated into the permit
(see the discussion below in this section).
After making a preliminary determination that the NOI meets the requirements of
40 CFR parts 122.21(i)(1) and 122.42(e), the Director has discretion as to how best to provide the
requisite public notification in the general permit context. For example, public notification could
be provided on the permitting authority’s website or through other electronic means. Another
alternative is to use the notice or fact sheet for the general permit to establish a procedure
allowing any person to electronically or by mail request notice of the receipt of an NOI, the
permitting authority’s proposed action, and the terms of the NMP proposed to be incorporated
into the permit. Those are appropriate ways to balance the competing concerns of providing
adequate notification to the public, providing flexibility to the permitting authority, and ensuring
the practicality of general permits. The permitting authority may provide notice of multiple NMPs
at one time provided that all applicable procedural and substantive permitting requirements
are satisfied. However, if the permitting authority chooses to provide notice, that notice must be
adequate, and the opportunity to comment must be meaningful.
Although the permit writer has broad discretion regarding how to write the minimum measures
as permit terms, to facilitate public review of the NMP the permit writer should decide how he
can clearly write the permit terms so they are easy to locate and are readily understood by the
permittee, permitting authority, and the public.
Under the regulations, the Director also has discretion to establish an appropriate period for
public review of the NOI and draft terms of the NMP proposed to be incorporated into the permit.
Under 40 CFR part 122.23(h)(1), the Director may establish by regulation or in the general permit
an appropriate period for the public to comment and request an appropriate period for the public
to comment and request an individual permit or a hearing. That differs from the specifications
in 40 CFR part 124.10, which sets a 30-day public notice period for proposed coverage under
individual permits. Having the Director set the period for public review by regulation or in
the general permit process allows the public and other interested parties an opportunity to
comment on the sufficiency of that period. Factors the permitting authority might consider when
3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage
3.4.2. General Permit

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NPDES Permit Writers’ Manual for CAFOs

establishing an appropriate period include the number of NOIs for which public notice is being
given at a time, the complexity of the material made available for public review, the expected
level of public interest based on prior notices of CAFOs seeking coverage, the opportunity for
the public to request an extension of the comment period for one or more facilities, and whether
individuals can request and receive individual notification of CAFOs seeking authorization to
discharge under the permit in a timely fashion.
As noted above, the Director must also provide an opportunity for the public to request a hearing.
40 CFR § 122.23(h)(1). The procedures for requesting and holding a hearing on the terms of
the NMP to be incorporated into the general permit are the same as those for draft individual
permits, which are provided in 40 CFR parts 124.11 through 124.13.
Once the processes for publicly reviewing the NMP and the terms of the NMP have been
completed, the Director must respond to all significant comments received during the comment
period. 40 CFR § 124.17. As necessary, the Director will require a CAFO owner or operator to
revise the NMP to address issues raised during the review process. Once the Director determines
3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage
3.4.2. General Permit

3-13

NPDES Permit Writers’ Manual for CAFOs

the CAFO’s NMP is complete, the Director must make the final decision whether to grant
permit coverage to the CAFO under the general permit. If coverage is granted, the Director must
incorporate the relevant terms of the NMP into the general permit and inform the CAFO owner
or operator and the public that coverage has been authorized and of the permit’s applicable
terms and conditions. 40 CFR § 122.23(h). Notification is necessary to ensure that the applicant
and interested individuals are aware of the Director’s final decision on granting authorization to
discharge under the general permit and incorporating site-specific NMP terms into the general
permit. Once a CAFO obtains authorization to discharge under an NPDES permit, it must
implement the terms and conditions of the NMP as incorporated in the permit, as of the date of
permit coverage authorization. 40 CFR § 122.42(e)(5).
Additional procedures are in place for EPA-issued general permits. For example,
40 CFR part 122.42(h)(2) requires the EPA Regional Administrator to notify each person who has
submitted written comments on the proposal of the decision to grant permit coverage and the
draft terms of the NMP of the final permit decision. A person affected by the general permit can
either challenge the general permit in court or apply for an individual permit as authorized in
40 CFR part 122.28.
The public notice process described above also includes providing notice to other affected states,
as required by the CWA. CWA section 402(b)(3) provides that the Administrator, in approving a
state program, should make sure that the state has adequate authority to ensure notice to “any
other state the waters of which may be affected.” Section 402(b)(5) provides that the Administrator
must ensure that any state “whose waters may be affected by the issuance of a permit may
submit written recommendations to the permitting state,” and that if those recommendations
are rejected, the permitting state must notify the affected state in writing of the reasons for the
rejection.
Any information submitted to the permitting authority as part of a permit application or NOI
must be made available for public review and comment, unless it is confidential business
information. 40 CFR § 122.7.

Endnotes
1

Table 3-1 lists the information that must be provided in permit application Forms 1 and 2B. B includes a copy of Form 2B.

3. Appropriate Permitting Strategies for CAFOs
3.1. NPDES CAFO Permit Applications and
Notice of Intent

3.2. Individual NPDES Permits for CAFOs

3.3. NPDES General Permits for CAFOs

3.4. Procedures for Permitting Authority
Review and Public Participation Before
Permit Coverage
3.4.2. General Permit

4-1

NPDES Permit Writers’ Manual for CAFOs

Chapter

4

4. Elements of an NPDES Permit
for a CAFO
The elements of an NPDES permit for a CAFO are the same as for those issued to other point
sources. The elements consist of a cover page, effluent limitations, monitoring and reporting
requirements, record-keeping requirements, special conditions, and standard conditions (see
Table 4-1). Each of those elements, other than the cover page, will be addressed in turn below as
each specifically relates to CAFOs. For additional details on the elements of an NPDES permit, see
EPA’s NPDES Permit Writers’ Manual (EPA-833-B-96-003).
Table 4-1. Elements of an NPDES Permit for a CAFO
Element

Section

Cover Page

Description
Serves as the legal notice of the applicability of the permit, identifies
the authority under which the permit is issued, and contains
applicable dates and signature(s).

Effluent
Limitations and
Standards

4.1

Serves as the primary mechanism for controlling discharges of
pollutants to receiving waters by identifying the specific narrative or
numeric limitations applied to the facility and the point of application
of these limits.

Monitoring
and Reporting
Requirements

4.2

Describes the types of monitoring to be performed, the frequencies
for collecting samples or data, how to record and maintain the data
and information, and how to transmit the required information to the
permitting authority.

Record-Keeping
Require­ments

4.2

Specifies the types of records to be kept on-site at the permitted
facility (e.g., inspection and monitoring records; waste and soil
sampling results; time, amount, and duration of land application
activities; precipitation records; records of recipients of waste
intended for application on land outside the operational control of
the CAFO facility, etc.).

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NPDES Permit Writers’ Manual for CAFOs

Table 4-1. Elements of an NPDES Permit for a CAFO (continued)
Element

Section

Description

Special
Conditions

4.3

In NPDES permits for CAFOs, special conditions must include
(1) the requirement to develop and fully implement an NMP, and
(2) the requirement that the NMP address nine minimum practices
defined in the regulation. In addition, NPDES permits for CAFOs
may include other special conditions as determined necessary by the
permitting authority.

Standard
Conditions

4.4

Conditions that are included in all NPDES permits, such as the
requirement to properly operate and maintain all facilities and
systems of treatment and control, as specified in 40 CFR part 122.41.

4.1. NPDES Effluent Limitations and Standards
Section 301(a) of the Clean Water Act (CWA) prohibits the discharge of pollutants from a point
source into waters of the U.S. unless the discharge complies with other provisions of the Act,
including the requirement for a discharge to be authorized under an NPDES permit. Effluent
limitations serve as the primary mechanism in NPDES permits for minimizing discharges of
pollutants to receiving waters. When developing effluent limitations for an NPDES permit, a
permit writer must include applicable technology-based effluent limits to control the pollutants.
CWA § 302(a). Technology-based effluent limits are included in NPDES permits to achieve a level
of treatment of pollutants for point source discharges on the basis of the applicable level of control
according to technologies specific to that industry. If technology-based limits are insufficient to
meet applicable water quality standards, the permit writer must include more stringent water
quality-based effluent limitations in the permit. CWA § 301(b)(1)(C).
This section addresses each type of limitation in turn.

4.1.1. Overview of Applicable Technology-Based Effluent
Limitations and Standards
Technology-based effluent limitations and standards for CAFOs must address all discharges
from a CAFO. 40 CFR § 122.42(e). As discussed below, technology-based standards are
established through a national ELG for some CAFO discharges. All other discharges must be
addressed through technology-based effluent limitations developed on a case-by-case basis by
the permit writer using her best professional judgement, or a combination of the two methods.
40 CFR § 125.3. (See the definition of best professional judgment [BPJ] in Section 4.1.4.) In general,
CAFO permits will include limits for process wastewater discharges from the CAFO’s production
area and land application area.
The production area at a CAFO includes the animal confinement areas and other parts
of the facility, including manure storage areas, raw materials storage areas, and waste
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.1. Overview of Applicable Technology-Based Effluent Limitations and Standards

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

containment areas. 40 CFR § 122.23(b)(8).
The land application area means all land
under the control of the CAFO owner or
operator, including where the CAFO owns,
rents, or leases the land to which manure
from the production area is applied.
40 CFR § 122.23(e)(3). It includes situations
where a CAFO determines when and how much
manure is applied to fields not owned, rented,
or leased by the CAFO.
The regulation at 40 CFR part 412 contains
the ELG applicable to CAFOs. The CAFO ELG
establishes the technology-based effluent
limitations and new source performance
standards (NSPS) for those operations that meet
the regulatory definition of a Large CAFO.1

Construction of a storage pond at a farm in Lonoke County,
Arkansas. (Photo courtesy of USDA/NRCS)

ELG Animal Sectors
Because the technology-based limits are developed on the basis of information concerning
different sectors in the industry, the ELGs for CAFOs are broken into the following subparts
addressing specific animal sectors:
▶ Subpart A: Horses and Sheep
▶ Subpart B: Ducks
▶ Subpart C: Dairy Cows and Cattle other than Veal
▶ Subpart D: Swine, Poultry, and Veal Calves
Table 4-2 provides a summary of the ELG applicable to each animal sector.
Table 4-2. Effluent limitation summary
Animal sector

ELG technology-based limits

Large CAFOs

40 CFR § 412

Subpart A—Horses and sheep

40 CFR § 412.13

Subpart B—Ducks

40 CFR § 412.22

Subpart C—Dairy cows and cattle other than veal calves

40 CFR §§ 412.33, 412.37
40 CFR §§ 412.45, 412.47

Subpart D—Swine, poultry, and veal calves

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.1. Overview of Applicable Technology-Based Effluent Limitations and Standards

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

All four subparts include specific discharge limitations. Subparts A and B contain technologybased requirements for the production area only. Subparts C and D include technology-based
requirements for both production areas and land application areas under the control of the
CAFO owner or operator. (For a discussion on the technology-based effluent limitations for Small
CAFOs, Medium CAFOs, and exotic animal species, see the discussion on BPJ in Section 4.1.4)

CAFOs That Are New Sources
The term new source is defined in 40 CFR part 122.2, and the criteria for determining a new source
is identified at 40 CFR part 122.29(b). Only Large CAFOs can be new sources subject to NSPS
requirements promulgated in accordance with CWA section 306 (as provided in 40 CFR part 412).
The new source criteria in 40 CFR part 122.29(b) are used to determine which Large CAFOs are
defined as new sources.

Regulatory Citation
New source means any building, structure, facility, or installation from which there is or could be a
discharge of pollutants, the construction of which began
(a) After promulgation of standards of performance under CWA section 306 that are applicable
to such a source, or
(b) After proposal of standards of performance in accordance with CWA section 306 that are
applicable to such a source, but only if the standards are promulgated in accordance with
section 306 within 120 days of their proposal. 40 CFR § 122.2.
Criteria for new source determination:
(a) Except as otherwise provided in an applicable NSPS, a source is a new source if it meets the
definition of new source in 40 CFR part 122.2, and
(i) It is constructed at a site at which no other source is located; or
(ii) It totally replaces the process or production equipment that causes the discharge of
pollutants at an existing source; or
(iii) Its processes are substantially independent of an existing source at the same site. In
determining whether those processes are substantially independent, the Director shall
consider such factors as the extent to which the new facility is integrated with the
existing plant; and the extent to which the new facility is engaged in the same general
type of activity as the existing source. 40 CFR § 122.29(b).

The first criterion for identifying a new source is construction of a new facility at a location where
no other source exists. Any Large CAFO that is newly built at a site where no other source exists
would be a new source CAFO subject to NSPS. In addition, an AFO that is constructed after
the establishment of the NSPS requirements that later expands to become a CAFO would be
considered a new source if it meets the criteria of 40 CFR part 122.29(b)(4).
The second criterion for defining a new source is where new construction at the facility replaces
the process or pro­duction equipment that causes the discharge of pollutants at an existing source.
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.1. Overview of Applicable Technology-Based Effluent Limitations and Standards

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

For CAFOs, that can include replacement
Regulatory Citation
of animal housing, an over­haul of
Construction of a new source as defined under
the facility’s production process, or a
40 CFR part 122.2 has commenced if the owner or operator has
substantial replacement of production
(a) Begun, or caused to begin as part of a continuous
equipment or waste-handling system
on‑site construction program:
that causes the dis­­charge of pollutants.
(i) Any placement, assembly, or installation of facilities
Confinement housing and barns at
or equipment; or
CAFOs are periodically replaced,
(ii) Significant site preparation work including clearing,
allowing the opportunity to install
excavation or removal of existing buildings,
improved systems that provide increased
structures, or facilities which is necessary for the
environmental protection. Modern
placement, assembly, or installation of new source
confinement housing used at many
facilities or equipment; or
swine, dairy, veal, and poultry farms
(b) Entered into a binding contractual obligation for the
is designed so the waste handling and
purchase of facilities or equipment which are intended to
storage generates little or no process
be used in its operation with a reasonable time. Options
water. Such systems negate the need
to purchase or contracts which can be terminated
for traditional flush systems and
or modified without substantial loss, and contracts
for feasibility engineering, and design studies do not
storage lagoons, reduce the risks of
constitute a contractual obligation under the paragraph.
uncontrollable spills, and decrease the
costs of transporting manure. Similarly,
40 CFR § 122.29(b)(4).
the replacement of an old dairy parlor
with a new one would likely result in the
facility being considered a new source, particularly where it is accompanied by a change in the
size of the dairy herd.
Third, a CAFO would be a new source if, when built, its production area and processes are
substantially independent of an existing source at the same site. For example, CAFOs could
construct new or additional production areas that are on one contiguous property, without
sharing waste management systems or commingling waste streams. Separate production
areas could also be constructed for biosecurity reasons. New production areas could also
be constructed for entirely different animal types, in which case, the more stringent NSPS
requirements for that animal subpart would apply to the separate and newly constructed
production area for any other subparts of animals. For example, a dairy could add a poultry
production facility that is, in fact, substantially independent of the dairy operation. In such a case,
the poultry operation would be a new source. In determining whether production processes and
waste-handling systems are substantially independent, the permitting authority should consider
factors such as the extent to which the new production areas are integrated with the existing
production areas, and the extent to which the new operation is engaging in the same general type
of activity as the existing source.
In some instances, such as the construction of a new Large CAFO, it is clear that the facility is a
new source. In other instances, such as where new equipment or a new waste handling system is
installed, the determination is a site-specific one that could turn on a number of factors. In such

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.1. Overview of Applicable Technology-Based Effluent Limitations and Standards

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

cases, the permitting authority should provide clear guidance to the facility concerning its status
if it is determined to be a new source.
Any new source CAFO is subject to the NSPS requirements applicable to the appropriate subpart
of part 412. 40 CFR § 412. The NSPS requirements for subparts A and B were not revised in the
2003 or 2008 CAFO rules. The NSPS requirements for subpart C were revised in 2003, and the
NSPS requirements for subpart D were revised in 2003 and again in 2008. The regulation at
40 CFR part 122.29(d) allows a 10-year protection period for new sources. That protection period
determines which facilities are subject to BAT and which are subject to NSPS depending on the
date of construction of the operation and for how long they may be subject to NSPS after the
promulgation of new NSPS standards. Table 4-3 describes the applicability of BAT and NSPS
requirements for operations under subparts C and D relative to when the facility was constructed
or defined as a CAFO.
Table 4-3. Applicability of NSPS for NPDES permits issued to CAFOs in subparts C and D
after promulgation of the revised CAFO regulations
Period that the Large CAFO began
construction [consistent with the
new source criteria in
40 CFR part 122.29(b)]

Do the BAT
requirements of
subparts C or D apply
to those facilities?

Do the NSPS
requirements of
subparts C or D apply
to those facilities?

(1) Large CAFOs that were defined
as CAFOs prior to the 2003
regulatory revisions and that began
construction before April 1993

Yes

No

(2) Large CAFOs that were defined
as CAFOs prior to the 2003
regulatory revisions and that began
construction between April 1993
and April 14, 2003 [note that actual
dates of the protection period
vary for each CAFO—as of July
2010, most are no longer in the
protection period]

Once the protection
period established by
40 CFR part 122.29(d)
expires, such CAFOs
are subject to the BAT
requirements of the ELGs.

Pre-2003 NSPS
requirements apply until
the end of the protection
period established by
40 CFR part 122.29(d).
Once the period expires,
the CAFO is subject to the
BAT requirements of the
ELGs.

(3) Existing AFOs that began
construction prior to April 14,
2003, and were newly defined as
Large CAFOs after the 2003 NPDES
regulatory revisions

Yes

No

(4) Large CAFOs subject to subpart C
that began construction after
April 14, 2003

No

Yes

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.1. Overview of Applicable Technology-Based Effluent Limitations and Standards

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

Table 4-3. Applicability of NSPS for NPDES permits issued to CAFOs in subparts C and D
after promulgation of the revised CAFO regulations (continued)
Period that the Large CAFO began
construction [consistent with the
new source criteria in
40 CFR part 122.29(b)]

Do the BAT
requirements of
subparts C or D apply
to those facilities?

Do the NSPS
requirements of
subparts C or D apply
to those facilities?

(5) Large CAFOs subject to subpart D
that began construction after
April 14, 2003, and before
December 4, 2008 [note that actual
dates of the protection period vary
for each CAFO]

Once the protection
period established by
40 CFR part 122.29(d)
expires, the CAFOs
are subject to the BAT
requirements of the ELGs.

2003 NSPS requirements
apply until the end
of the protection
period established by
40 CFR part 122.29(d).
Permitting Authority may
establish more stringent
requirements. Once the
period expires, the CAFO
is subject to BAT under
the newly promulgated
guideline.

(6) Large CAFOs subject to subpart D
that began construction after
12/04/08

No

Yes

For a detailed discussion of NSPS requirements by subpart see, Section 4.1.2. New Source
Performance Standards – Subpart C and D.
Where EPA is the permitting authority, a new source permit for a CAFO subject to NSPS (as
identified in Table 4-3) is subject to review under the National Environmental Policy Act (NEPA),
42 U.S.C. § 4321 et seq. Depending on the circumstances associated with the facility or facilities
covered by the permit and the requirements of the permit, NEPA requirements may be satisfied
by completing an environmental impact statement (EIS) or an environmental assessment (EA).
An EA may be used where there is a finding of no significant impact (FONSI). Federal permit
writers should coordinate efforts with the Office of Federal Activities and document all NEPA
activities in the permit file and fact sheet.

CAFOs That Are New Dischargers
An AFO that is (1) newly constructed; (2) implements changes so that it meets the definition of
a CAFO; or (3) that is designated as a CAFO is a new discharger if it is not a new source. A new
discharger is an AFO that becomes a CAFO either through definition or designation and is not
a new source (i.e., subject to NSPS). Such operations could be a CAFO for one of the following
reasons: (1) the facility is newly constructed (but not subject to NSPS and therefore not a new
source); (2) the facility has changed some aspect of its operations such that it becomes defined as

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.1. Overview of Applicable Technology-Based Effluent Limitations and Standards

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

a Medium CAFO or designated as a Small or Medium CAFO. The following are examples of such
operations:
▶ A newly constructed Medium CAFO operation. Because the CAFO NSPS apply only to
Large CAFOs, such a facility would not be subject to NSPS but would be subject to BPJ/
BCT and BAT requirements. However, if the facility later expands to become a Large
CAFO, the facility would likely be considered a new source, because construction
began after the applicable NSPS requirements were established.
▶ An existing operation that increases the number of animals confined and thus meets
the threshold numbers to be defined as a Large CAFO but is determined to not meet
any of the new source criteria. It is subject to the ELGs requirements applicable to its
subcategory.
▶ An existing operation that increases the number of animals confined and thus meets
the threshold capacity to be defined as a Large CAFO.

4.1.2. Technology-Based Requirements for the Production
Area of Large CAFOs
Operations Covered by Subpart A—
Horses and Sheep
The ELG requirements for subpart A, 40 CFR subparts 412.10-15,
address the production area only. Any additional technologybased requirements for discharges from the CAFO must be
developed using BPJ.
Existing and new Large CAFOs that confine horses and sheep
may not discharge manure or process wastewater (which
includes horse washdown water) pollutants to waters of the U.S.
from the CAFO (i.e., no-discharge standard). The only exception
to the no-discharge standard is an overflow that occurs because
of a rainfall event from a facility that is designed, constructed,
operated, and maintained to contain all process wastewater
plus the runoff from a 25-year, 24‑hour rainfall event for the
location of the CAFO. 40 CFR §§ 412.13, 412.15.

Flock of sheep near Dubois, Idaho.
(Photo courtesy of USDA/NRCS)

To ensure that a facility meets the no-discharge standard, the
CAFO must ensure that the production area has adequate
storage structures that are designed, constructed, operated,
and maintained to contain all manure including the runoff
and direct precipitation from a 25-year, 24-hour rainfall event.
An important consideration as to whether the CAFO meets

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.2. Technology-Based Requirements for the Production Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

the ELG requirements is whether it has adequate
storage or treatment structures capable of containing
all manure, litter, and process wastewater that
accumulates during the critical storage period.
40 CFR § 412.13. To comply with the ELG, the storage
volume in the production area must contain all those
wastes. For a detailed discussion on adequate storage
of manure, see Section 5.3.

Regulatory Citation
Overflow means the discharge of manure or process
wastewater resulting from the filling of wastewater
or manure storage structures beyond the point at
which no more manure, process wastewater, or
stormwater can be contained by the structure.
40 CFR § 412.2(g)

Operations Covered by Subpart B—Ducks
The ELG requirements for subpart B, 40 CFR part 412.20-26, address the production area only. The
ELG distinguishes between two types of manure handling systems in the production area of duck
operations (wet lot and dry lot). Chapter 2.2.4. explains the difference between wet lot and dry lot
manure handling systems. Any additional technology-based requirements for discharges from
the CAFO must be developed on a BPJ basis. 40 CFR § 125.3(a).
All duck operations constructed before 1974 subject to the ELG must meet specific discharge
limitations established by 40 CFR part 412.22. Those are the only numeric limitations in the CAFO
ELGs. The limitations are shown in Table 4-4.
Table 4-4. Numeric effluent limitations for subpart B—Ducks

Regulated parameter
BOD5
Fecal coliform

Maximum
dailya

Maximum
monthly
averagea

Maximum
dailyb

Maximum
monthly
averageb

3.66

2.0

1.66

0.91

(c)

(c)

(c)

(c)

Notes:
a. Pounds per 1,000 ducks
b. Kilograms per 1,000 ducks
c. Not to exceed MPN of 400 per 100 mL at any time

All duck CAFOs constructed after 1974 are new sources subject to a no-discharge standard that is
identical to the BAT standard for subpart A (Horses and Sheep). 40 CFR § 412.25. Subpart B CAFOs
may not discharge process wastewater pollutants into waters of the U.S., except for an overflow
of process wastewater caused by rainfall events from a facility that was designed, constructed,
operated, and maintained to contain all process generated wastewater plus the runoff from a
25‑year, 24-hour rainfall event. 40 CFR §§ 412.25(b), 26(b).
To ensure that a facility meets the no-discharge standard, the CAFO must ensure that the
production area has adequate storage structures that are designed, constructed, operated, and
maintained to contain all manure, litter, and process wastewater including the runoff and direct
precipitation from a 25-year, 24-hour rainfall event. An important consideration as to whether the
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.2. Technology-Based Requirements for the Production Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

CAFO meets the ELG requirements is if it has adequate storage or treatment structures capable of
containing all manure, litter, and process wastewater that accumulate during the critical storage
period. To comply with the ELG, the storage volume in the production area must contain all those
wastes. For a detailed discussion on adequate storage of manure, see Section 5.3.

Operations Covered by Subpart C—Dairy Cows and Cattle Other
than Veal Calves and by Subpart D—Swine, Poultry and Veal Calves
Existing Sources—Subparts C and D
The ELG requirements for subparts C and D, 40 CFR subparts 412.30-37, 412.40-47, address both
the production area and the land application area. This section addresses the technology-based
requirements associated with the production area. Subpart C includes requirements for Large
CAFOs that confine dairy cattle and cattle other than veal calves, and subpart D includes Large
CAFOs that confine swine, poultry and veal calves. The requirements in subpart C are identical
for existing sources and new sources. The requirements in subpart D differ for existing and new
sources. The new source requirements for subpart D are addressed below.
Existing sources subject to subparts C and D and new sources subject to subpart C are subject
to a no-discharge requirement. Those operations may not discharge manure into waters
of the U.S. from the production area. 40 CFR §§ 412.31(a), 412.32(a), 412.33(a) (subpart C),
40 CFR §§ 412.43(a), 412.44(a), 412.45(a) (subpart D). The only exception to that no-discharge
standard is when precipitation causes an overflow, provided that the production area is designed,
constructed, operated, and maintained to contain all manure, litter, and process wastewater
including the runoff and direct precipitation from a 25-year, 24-hour rainfall event (see the
definition of overflow).
To ensure that a facility meets the no-discharge standard, the CAFO must ensure that the
production area has adequate storage structures that are designed, constructed, operated, and
maintained to contain all manure, litter, and process wastewater including the runoff and direct
precipitation from a 25-year, 24-hour rainfall event. An important consideration of whether the
CAFO meets the ELG requirements is whether it has adequate storage or treatment structure
capable of containing all manure, litter, and process wastewater that accumulate during the
critical storage period. To comply with the ELG, the storage volume in the production area must
contain all those wastes. For a detailed discussion on adequate storage of manure, see Section 5.3.
To meet the no-discharge requirement, the CAFO must operate the production area in
accordance with additional measures and record-keeping requirements specified in
40 CFR parts 412.37(a)-(b), 412.47(a)-(b). Those include requirements for routine visual
inspections of the production area, the use of depth markers for liquid impoundments, corrective
action when deficiencies are identified, and mortality handling. Records must be maintained onsite, including records for each of the above measures, and records documenting the design of
storage structures and any overflows that occur.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.2. Technology-Based Requirements for the Production Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

Voluntary Performance Standards
The voluntary alternative performance standards provisions in 40 CFR part 412.31(a)(2)
also apply to existing sources subject to subpart
C and D and new sources subject to subpart C.
(See Appendix F, Voluntary Alternative Performance Standards for CAFOs, of this Manual.)2
This provision applies only to discharges
from the production area. The provision for
alternative performance standards allows a
CAFO owner or operator to request from the
Director NPDES permit effluent limitations
according to site-specific alternative
technologies where the CAFO can establish
Holstein dairy cows. (Photo courtesy of USDA/ARS)
that the alternative technologies will achieve
a quantity of pollutants discharged from the
production area equal to or less than the quantity of pollutants that would be discharged under
applicable baseline effluent guidelines performance standards.
The production area baseline for existing sources subject to subparts C and D and new sources
subject to subpart C prohibits the discharge of manure except when rainfall events cause an
overflow from a storage structure designed, constructed, operated, and maintained to contain
all manure plus the runoff and direct precipitation from a 25-year, 24-hour rainfall event.
40 CFR §§ 412.31(a), 412.32(a), 412.33(a) (subpart C), 412.43(a), 412.44(a), 412.45(a) (subpart D).
Thus, a Large CAFO seeking permit conditions according to a voluntary alternative performance
standard would have to first establish the predicted discharge on the basis of the baseline effluent
guidelines and second, establish that its alternative technologies and management practices
result in equivalent or improved pollutant reductions for the production area. In meeting each of
those requirements, the CAFO must submit technical analyses and other relevant information
and data specified in the regulation. Because the production area baseline provides for no
discharge except in specified circumstances, the alternative standard must take into account
those circumstances where discharges do occur under the baseline (i.e., extreme rainfall events).
When meeting those requirements, the regulations require calculation of the median annual
overflow volume on the basis of an extended period (25 years) of actual rainfall data (and then
calculating a predicted average annual discharge of pollutants).
Large CAFOs seeking permit conditions that are based on the voluntary performance standards
must still meet any other applicable federal, state, and local requirements (see Appendix F,
Voluntary Alternative Performance Standards for CAFOs). Because using voluntary alternative
performance standards is typically contemplated for discharging systems, it is important to keep
in mind that any allowable discharges might be subject to other requirements, notably water

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.2. Technology-Based Requirements for the Production Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

quality-based standards, and more stringent state requirements. (For a discussion on water
quality-based effluent limitations, see Section 4.1.9)
The permit writer must determine which ELG requirements the alternative standard replaces
and which remain intact and applicable to all CAFOs. Under the alternative standard, the
management practices and additional measures specified in the effluent guidelines that
apply to the production area and land application area remain applicable to all Large CAFOs.
40 CFR §§ 412.4, 412.37, 412.47. Conversely, other requirements might no longer be applicable
because of the alternative performance standard. For example, if under an alternative
performance standard the operation does not have a liquid storage structure, the depth marker
requirement would no longer be applicable.

New Source Performance Standards—Subparts C and D
As discussed in the previous section, Large subpart C beef and dairy CAFOs that are new
sources have the same production area requirements as existing subpart C operations.3 Large
subpart D swine, poultry, and veal calf CAFOs that are new sources are subject to the NSPS.
40 CFR § 412.46. Like existing sources subject to subpart D, new sources under subpart D may not
discharge manure, litter, or process wastewater into waters of the U.S. from the production area
and are required to comply with the additional measures and record-keeping requirements at
40 CFR parts 412.47(a), (b).
Unlike the requirements for existing sources, 40 CFR part 412.46 does not allow an exception
for new sources to the no discharge requirement. Rather, a CAFO subject to the requirements
of 40 CFR part 412.46 must either (1) have an absolute prohibition of any discharge from its
production area as a condition of its permit, or (2) request the permitting authority to “establish
NPDES best management practice effluent limitations designed to ensure no discharge…”
whereby the facility can satisfy the no discharge effluent limitation. 40 CFR § 412.46(a)(1).
A site-specific effluent limitation established in accordance with 40 CFR part 412.46(a)(1) must
address the CAFO’s entire production area. For any CAFO using an open surface manure
storage structure, the no-discharge standard used in 40 CFR part 412.46 “means that the storage
structure is designed, operated, and maintained in accordance with best management practices
established by the Director on a site-specific basis after a technical evaluation of the storage
structure.” 40 CFR § 412.46(a)(1). The technical evaluation must be based on information used in
the design of the storage structure necessary to meet the NSPS requirements, including minimum
storage periods for rainy seasons; additional minimum capacity for chronic rainfalls; applicable
technical standards that prohibit or otherwise limit land application to frozen, saturated, or
snow-covered ground; planned emptying and dewatering schedules consistent with the CAFO’s
NMP; additional storage capacity for manure intended to be transferred to another recipient
later; and any other factors that would affect the sizing of the open manure storage structure.
40 CFR § 412.46(a)(1)(i). (For further discussion of adequate storage, see Section 5.3.)

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.2. Technology-Based Requirements for the Production Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

Part 412.46(a)(1)(ii) requires that the technical evaluation include an evaluation of the adequacy
of the design of the open manure storage structure using the most recent version of the Natural
Resources Conservation Service’s (NRCS’s) AWM tool and an evaluation of the overall water
budgets using SPAW Field and Pond Hydrology Tool, or equivalent analytic tools (see Appendix N,
References for NPDES Permit Writers). 40 CFR § 412.46(a)(1)(i). Where 100 years of continuous
rainfall data are not available for all CAFOs, models can be run using actual rainfall data where
available, and then simulated with a confidence interval analysis over a period of 100 years.
AWM tracks gross nutrients, but it does not track the mass or concentration of nutrients. Further,
the storage period or drawdown schedule is usually determined by the individual CAFO.
Accordingly, in conducting the technical evaluation, the CAFO’s NMP must be used as an input
to confirm both a water balance and a nutrient balance has been achieved by the CAFO. The
NSPS provisions require that each CAFO use the SPAW model (or equivalent approved by the
permitting authority) to assess daily hydrologic budgets for each field. The complete modeling
demonstration shows not only that the storage facility does not discharge, but also that there
is no runoff of process wastewater from fields during land application activities consistent
with the CAFO’s NMP. Those calculations are necessary to ensure that the open containment
system is operated in a way to meet land application requirements of 40 CFR part 412.46(b).
The requirement to use the SPAW model (or equivalent tool) ensures that CAFOs will rely on
appropriate operational measures to achieve no discharge standards.
The CAFO NSPS provisions require certain specified information regarding design, construction,
and operation and maintenance (O&M) of the system to be included in the CAFO’s NMP. That
includes the key user-defined inputs and model system parameters. CAFOs must submit a sitespecific analysis to the Director. 40 CFR § 412.46(a)(1). The site-specific design, construction,
and O&M measures are enforceable requirements of the CAFO’s permit. As long as the CAFO
complies with the requirements, the CAFO is presumed to meet the no-discharge requirement,
such that, if a discharge occurs, the CAFO may rely, to the extent they are applicable, on the
NPDES upset and bypass provisions of 40 CFR parts 122.41(m), (n).
Under NSPS, the Director has the discretion to require additional information from a new source
subpart D CAFO owner or operator to support site-specific BMP effluent limitations. The burden
is on the CAFO to demonstrate that any proposed system it employs, including an open system,
meets the new source standard. CAFOs are encouraged to use the most current version of AWM
and SPAW when submitting their demonstration to the permitting authority. However, EPA is
aware that other peer-reviewed models and programs have been or could be developed that
the permitting authority could determine are equivalent to AWM and SPAW. The Director may
approve design software or procedures that are equivalent to AWM and SPAW. Once approved by
the Director, the public still would have the opportunity to comment on the CAFO’s modeling.
The design parameters and evaluation process required of all CAFOs wishing to avail themselves
of the alternative is intended to allow CAFOs the flexibility to demonstrate compliance with the
no-discharge requirements for any type of open storage facility. As a practical consideration, it
is expected that most CAFOs selecting the compliance alternative will submit designs for open
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.2. Technology-Based Requirements for the Production Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

manure storage structures accompanied by a narrow range of acceptable operation and management practices. However, for a given type of storage facility design (for example, an integrator with
several company-owned CAFOs, each designed and constructed in an essentially identical manner within the same county), an operator may conduct a series of assessments that together fully
encompass the range of operational and management measures that would be used across multiple
CAFOs with the specific storage facility design (i.e., types of crops, soil types and other field para­
meters, land application and other equipment, timing and land application schedules). In such
a case, SPAW could be run to validate a wide range of NMP and storage pond management. This
alternative does not affect the requirement for a CAFO to develop a site-specific NMP. The NSPS
requirements allow the permitting authority to determine that CAFOs that have a specified facility
type and submit an NMP that falls within the preapproved range of operational and management
practices would not need to conduct an individualized assessment (i.e., the validation using SPAW).
The availability and use of such a geographical and categorical approach would require that the
permit writer determine that a number of conditions are met. First, the assessment would need
to fully account for all pertinent factors relevant to determining the potential for a discharge from
an open storage system. The assessment would also need to include all parameters that mirror
the range of soil, plant, climatic, and hydrological conditions in the representative geographical
area. Finally, the assessment would need to reflect the operational and management practices to
be employed by each CAFO at each individual site. Each CAFO must have a site-specific NMP that
includes the operational and management measures used in the geographical assessment.
New sources subject to subpart D using an open storage structure must have a depth marker to
indicate the maximum volume of manure and process wastewater the structure is designed to
contain (whereas existing sources and new sources subject to subpart C must use a depth marker
that indicates the 25-year, 24-hour storm event).
An important consideration of whether a CAFO meets the NSPS alternative is if it has an adequate
storage or treatment structure capable of containing all manure that accumulates during the
critical storage period. To comply with the NSPS, the storage volume in the production area must
contain all wastes. For a detailed discussion on adequate storage of manure, see Section 5.3.

4.1.3. Technology-Based Requirements for the Land
Application Area of Large CAFOs
Each CAFO subject to the ELG requirements in subparts C and D that land applies manure
must do so in accordance with certain practices that constitute the technology-based effluent
limitations for the land application area. 40 CFR §§ 412.4, 412.37(c).
A general description of the practices required by 40 CFR part 412.4 follows (for additional
discussion of the requirements for nutrient management practices see Chapters 5 and 6):
▶ Develop and implement a field-specific NMP that fully incorporates the other
requirements of 40 CFR part 412.4 concerning land application.
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.3. Technology-Based Requirements for the Land Application Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

▶ Land apply manure at application
rates that minimize nitrogen and
phosphorus transport from the field to
waters of the U.S. in compliance with
the technical standards for nutrient
management established by the
permitting authority. The technical
standard for nutrient management
must include a field-specific
assessment of the potential for nitrogen
and phosphorus transport from the
field to waters of the U.S. and address
the form, source, amount, timing, and
method of application of nutrients
on each field to achieve realistic
Landowner and an NRCS staff member discuss management
options for the land application area.
production goals while minimizing
(Photo courtesy of USDA/NRCS)
nitrogen and phosphorus movement
to waters of the U.S. The standard must
also include appropriate flexibility for
any CAFO to implement nutrient management practices to comply with the standard
such as consideration of multiyear phosphorus applications to fields that do not have a
high potential for phosphorus runoff to waters of the U.S. and phased implementation of
phosphorus-based nutrient management, as determined appropriate by the Director.
▶ Analyze manure at least once a year for nitrogen and phosphorus content, and analyze
soil at least once every 5 years for phosphorus content. The results of the analyses
are to be used in determining application rates for manure, litter, and other process
wastewater.
▶ Periodically inspect equipment used for land application of manure for leaks (before
each application is recommended to ensure the manure is delivered at the proper rate
of application).
▶ Implement a minimum setback for manure application of 100 feet from surface waters
and conduits to surface waters; or substitute with a 35-foot vegetated buffer, or other
alternatives where the CAFO demonstrates equivalent pollutant reductions.
▶ Complete on-site records documenting implementation of all required best
management practices (BMPs) and any additional records specified by the permitting
authority (for additional information, see Section 4.2).
Many states have unique requirements for developing an NMP. The requirements of EPA
regulations establish the minimum requirements for permitted CAFOs. States may require
more stringent requirements, and in many instances states have established additional
requirements to address land application. For example, many states require more frequent soil
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.3. Technology-Based Requirements for the Land Application Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-16

NPDES Permit Writers’ Manual for CAFOs

analysis than is required by 40 CFR part 412.4(c)(3). In recognition of that, 40 CFR part 412.4(c)(2)
requires application rates for land application of manure, litter, and process wastewater to be
in compliance with technical standards for nutrient management established by the Director.
Part 123.36 requires that the state’s technical standards be a part of every approved state’s NPDES
program. 40 CFR § 123.36. EPA strongly encourages states, when establishing their technical
standards for nutrient management, to address water quality protection issues when determining
appropriate land application practices. At a minimum, the permitting authority must include in
the technical standard the following components:
▶ A field-specific assessment of the potential for nitrogen and phosphorus transport from
the field to waters of the U.S.
▶ The form, source, amount, timing, and method of application of nutrients on each
field to achieve realistic production goals, while minimizing nitrogen and phosphorus
movement to waters of the U.S.
▶ Appropriate flexibility for CAFOs to implement the standard (e.g., multiyear
phosphorus banking.)
40 CFR § 412.4(c).
The state technical standards will provide additional specificity to key nutrient management
provisions in the ELG. The standards should include additional information, such as soil and
manure sampling and analysis protocols, application methods, and plan content requirements.
State and tribal technical standards for nutrient management are typically developed collectively
among the agencies responsible for various aspects of the nutrient management planning in a
state, including the respective NPDES permitting authorities, state departments of agriculture,
tribes, state land grant universities, NRCS state conservationists, and EPA Regions. Many technical
standards for nutrient management have already been developed as part of implementing U.S.
Department of Agriculture’s (USDA’s) National Nutrient Management policy. NRCS developed
a national nutrient management conservation practice standard (Code 590) that serves as the
basis for each state NRCS office to develop its owned tailored standard. In many cases, the NRCS
state standards have formed the basis for the standard established by the permitting authority.
However, state technical standards established by the Director to meet NPDES requirements must
address the criteria specified in 40 CFR part 412.4(c)(2). State technical standards are subject to
review and approval by EPA under 40 CFR part 123.62. When establishing the technical standards,
the Director may use discretion regarding the means of expressing and documenting the
standards (i.e., as law, regulations, or policy) for use by CAFOs and technical standard providers in
developing NMPs, for permit writers and the public in reviewing NMPs, and for submission to EPA
as part of the state authorized NPDES program pursuant to the requirements of 40 CFR part 123.36.
(For a detailed discussion on state technical standards, see Section 6.3.1)
The ELG also specifies that manure must be analyzed at a minimum once every year for nitrogen
and phosphorus, and the soil must be analyzed at a minimum once every 5 years for phosphorus.
40 CFR § 412.4(c)(3). The analytical results are to be used in determining application rates for
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.3. Technology-Based Requirements for the Land Application Area of Large CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-17

NPDES Permit Writers’ Manual for CAFOs

manure. More frequent analyses than required by the ELG might be needed to ensure appropriate
agricultural utilization of the applied nutrients. The actual sample collection process and
frequency should be established in the CAFO’s NMP in accordance with the technical standards
for nutrient management.
Finally, the ELG specifies that the site-specific conservation practices for a permitted Large CAFO
must include maintaining a 100-foot setback or establishing a 35-foot vegetated buffer between
land application areas and any downgradient surface waters, open tile line intake structures,
sinkholes, agricultural well heads, or other conduits to surface waters. 40 CFR § 412.4(c)(5). The
ELG allows for compliance alternatives in place of the setback or buffer under certain scenarios.
Those and other requirements applicable to permitted Large CAFO requirements are described in
greater detail in Chapters 5 and 6.

4.1.4. Best Professional Judgment (BPJ)
NPDES permit limitations are based on BPJ
when national ELGs have not been issued
pertaining to an industrial category or process.
Specifically, the NPDES regulations require a
permit writer to establish permit limitations
on a case-by-case BPJ basis when ELGs are
inapplicable, or in combination with the effluent
guidelines, where the ELG apply to only certain
aspects of the operation or certain pollutants.
CWA § 402(a)(1); 40 CFR § 122.44(k).
As explained in Section 4.1.1, ELGs have been
promulgated for only those operations that meet the
Alpaca farm. (Photo courtesy of USDA/MO NRCS)
regulatory definition of a Large CAFO, and apply
to the production area for subparts A, B, C, and D,
and land application area for subparts C and D. For example, there is no ELG for Small or Medium
CAFOs or for exotic animal species. Exotic animal species are those not specifically identified in the
ELG, for example: llamas, geese, or ostriches. Nonetheless, just as for any other permitted facility,
the CWA requires that an NPDES permit for small, medium, and exotic animal CAFOs include
technology-based effluent limitations. Therefore, the technology-based limits in the permit must be
determined by the permit writer using BPJ (see Table 4-5).
Table 4-5. Facilities where the technology-based limits must be developed using BPJ
Animal Sector
Medium CAFOs—Horses, sheep, duck, dairy cows, cattle, swine, poultry, and veal calves
Small CAFOs—Horses, sheep, duck, dairy cows, cattle, swine, poultry, and veal calves
Other CAFOs—Alligators, geese, emus, ostriches, mink, bison, etc.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.4. Best Professional Judgment (BPJ)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

Similarly, for any part of a permitted facility from which there could be an authorized discharge,
but for which there is no applicable ELG, technology-based limits must be set using BPJ.
That includes any part of a CAFO not addressed by the land application or production area
requirements of the ELG, even where the ELG address some parts of the CAFO operation. For
example, land application areas at large horse, sheep, or duck CAFOs, which are not subject
to the ELG requirements of 40 CFR part 412.4 but are required to have an NMP that meets the
requirements of 40 CFR part 122.42(e)(1). It also includes any other discharges from CAFOs
subject to subparts C and D that are not addressed by the ELG.
For all Small and Medium CAFOs, exotic animal species, and areas of Large CAFOs not addressed
by the ELG, the permit writer can develop effluent limits on a case-by-case basis using the permit
writer’s BPJ. The term case-by-case has been understood to mean on a permit-by-permit basis
so as to allow the use of general permits that include BPJ limits. It is important to note in such a
context that a CAFO is not required to seek coverage under a general permit and always has the
option to apply for an individual permit. The authority to issue case-by-case permit limitations
comes from CWA section 402(a)(1) and 40 CFR parts 122.44(a), 125.3.
Given the similarity in the operational characteristics of CAFOs, in many cases, permit writers
might find that it is appropriate to develop BPJ effluent limitations that are the same as, or similar
to, the effluent limitations established in the ELG. See 40 CFR part 125.3. For example, a permit
writer might decide that the most appropriate limitations for Medium and Small CAFO permits
are the same as some of or all the requirements established for Large CAFOs in the ELG. On the
other hand, a permit writer may establish different technology-based limitations for Medium
and Small CAFOs using his or her BPJ, such as the site-specific circumstances that resulted in
the small or medium-size AFO being defined or designated a CAFO. BPJ requirements based on
the ELG should include requirements for the production area and the land application area and
should include specific record-keeping requirements.
For all CAFOs, there are other circumstances where a permit writer must use BPJ or special
permit conditions to address specific discharges at a CAFO that are not included in the ELG. For
example, the CAFO ELG does not address plate chiller water, filter backwash water, chemicals
used in the production area (for disinfection), or pollutants (such as manure, feathers, and feed)
that have fallen to the ground immediately downward from confinement building exhaust
ducts and ventilation fans and are carried by precipitation-related or other runoff to waters
of the U.S. The permit must address technology-based limitations for those discharges on a
BPJ determination, and more stringent water quality-based limits where necessary to ensure
compliance with water quality standards. CWA § 402(a)(1). The same requirements apply to
discharges that constitute stormwater discharges associated with industrial activities subject to
40 CFR part 122.26(b)(14) (see discussion on other discharges in Section 4.1.5).

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.4. Best Professional Judgment (BPJ)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

40 CFR part 125.3(c): Methods of imposing technology-based treatment requirements in permits. Technology-based
treatment requirements may be imposed through one of the following three methods:
(1) * * * * *
(2) On a case-by-case basis under section 402(a)(1) of the Act, to the extent that EPA-promulgated effluent
limitations are inapplicable. The permit writer shall apply the appropriate factors listed in 40 CFR part 125.3(d)
and shall consider: (i) The appropriate technology for the category or class of point sources of which the
applicant is a member, based upon all available information; and (ii) Any unique factors relating to the applicant.
[Comment: These factors must be considered in all cases, regardless of whether the permit is being issued by
EPA or an approved State.]
(d) In setting case-by-case limitations pursuant to 40 CFR part 125.3(c), the permit writer must consider the
following factors:
(1) For BPT requirements: * * * * *
(2) For BCT requirements: (i) The reasonableness of the relationship between the costs of attaining a reduction
in effluent and the effluent reduction benefits derived; (ii) The comparison of the cost and level of reduction
of such pollutants from the discharge from publicly owned treatment works to the cost and level of reduction
of such pollutants from a class or category of industrial sources; (iii) The age of equipment and facilities
involved; (iv) The process employed; (v) The engineering aspects of the application of various types of
control techniques; (vi) Process changes; and (vii) Non-water quality environmental impact (including energy
requirements).
(3) For BAT requirements: (i) The age of equipment and facilities involved; (ii) The process employed; (iii) The
engineering aspects of the application of various types of control techniques; (iv) Process changes; (v) The
cost of achieving such effluent reduction; and (vi) Non-water quality environmental impact (including energy
requirements).

4.1.5. Industrial Stormwater
Discharges4
CAFOs are subject to industrial stormwater
permitting requirements of 40 CFR part 122.26.
Large CAFOs, as defined in 40 CFR parts 122.23
and 412 are included in category (i) of facilities
considered to be engaging in industrial
activity under part 122.26 (b)(14), which
defines 15 categories of “storm water discharge
associated with industrial activity.” See
40 CFR part 122.26(b)(14)(i); NPDES Storm
Water Program Question and Answer Document
Volume 1 (USEPA 1992). As a result, Large CAFOs
are subject to the requirements of part 122.26
regardless of whether they are a permitted
facility under part 122.23. The requirements of

NRCS District Conservationist suggests filter strip as one
option to protect the land and improve water quality.
(Photo courtesy of USDA/NRCS)

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.5. Industrial Stormwater Discharges

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-20

NPDES Permit Writers’ Manual for CAFOs

part 122.26 apply to any stormwater discharge associated with industrial activity at a Large CAFO
that is not otherwise regulated under parts 122.23 and 412.
CAFOs that are permitted to discharge pursuant to 40 CFR parts 122.23 and 122.26 may have both
sets of requirements included in a single permit or in separate wastewater and stormwater permits.
CAFOs subject to part 122.26 requirements may qualify for the conditional exclusion provided in
part 122.26(g) for no exposure certifications for stormwater discharges.
CAFOs may also be subject to stormwater permitting requirements for construction activity
under 40 CFR parts 122.26(b)(14)(x) or 122.26(b)(15).

4.1.6. Other Technology-Based Limitations that Apply to
Discharges from CAFOs
CAFOs may have additional discharges not specifically addressed in the ELG or CAFO
regulations, either from the production area or from outside the production area. Those include
but are not limited to the following:
▶ Process wastewater discharges from outside the production area, such as washdown
of equipment that has been in contact with manure, raw materials, products or byproducts that occurs outside the area.
▶ Discharges that do not meet the definition of process wastewater, such as domestic
wastewater discharges; chiller water; discharges associated with feed, fuel, chemical,
or oil spills, and equipment repair.
▶ Discharges of pollutants from poultry,
swine, and veal calf animal confinement
houses that are not covered by the
ELG. Those include removal of animals
and cleaning out houses, and runoff
associated with fan exhaust deposits
outside the houses.

Where appropriate, permit writers should consider writing
technology-based limitations for runoff associated with fan
exhaust deposits outside a poultry house.
(Photo courtesy of USDA/NRCS)

A properly written CAFO permit will address
discharges such as those and establish BAT/
BCT limits developed on a BPJ basis (as
discussed in Section 4.1.4). The determination
of whether to apply the no-discharge standard
to areas other than those that are covered by
the ELG (animal confinement area, manure
storage area, waste containment area, and
so on) is a site-specific determination that
must be made by the permitting authority.
EPA and states can begin the BPJ analysis

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.6. Other Technology-Based Limitations that Apply to Discharges from CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

with an evaluation based on the no-discharge standard, because that is the applicable standard
most closely related to those facilities (see discussion of BPJ-based limits in Section 4.1.4). (For
an example of limitations on other discharges from CAFOs, see the example general permit in
Appendix J, NPDES General Permit Template for CAFOs.) If other measures are appropriate, they
may be identified in the permit and subject either to conditions applicable to all permittees or
addressed on a site-specific basis, perhaps in conjunction with the CAFO’s NMP. It should be
noted that any such discharges are also subject to applicable water quality standards.

4.1.7. Nutrient Management Plan (NMP)
An NMP is a detailed planning document that identifies conservation practices and management
activities that, when implemented, help to ensure that both production and natural resource
protection goals are achieved. The objective of an NMP is to document those practices and
activities that will help achieve the goals of the producer and protect or improve water quality.
An NMP that is part of a CAFO permit must include, at a minimum, BMPs necessary to achieve
the nine minimum requirements of 40 CFR parts 122.42(e)(1)(i)-(ix) (minimum measures) and
other effluent limitations and standards, to the extent applicable, which are described in greater
detail in Chapters 5 and 6. 40 CFR § 122.42(e)(1).
The minimum measures include requirements
applicable to both the production area and the
land application area. See Appendix H, NPDES
CAFO Nutrient Management Plan Review
Checklist.
As discussed in Chapter 3.2, CAFOs must submit
a site-specific NMP to the permitting authority
as part of their permit application or NOI when
they are seeking permit coverage. The permitting
authority may require the CAFO operator to
make changes to its NMP before permit coverage
is granted. 40 CFR § 122.23(h). Once coverage is
granted, the permittee must implement the NMP
approved by the Director.

Creating a nutrient management plan.
(Photo courtesy of USDA/MO NRCS)

Minimum Measures that Must be Terms and Conditions of the
NPDES Permit
Every NPDES permit issued to a CAFO must require that the CAFO implement the terms of a
site-specific NMP approved by the Director. 40 CFR § 122.42(e)(5). Those site-specific terms of
the NMP are defined as “the information, protocols, [BMPs], and other conditions” identified
in a CAFO’s NMP and determined by the permitting authority to be necessary to meet the
requirements of 40 CFR part 122.42(e)(1). 40 CFR § 122.42(e)(5). To meet those requirements,
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

the information, protocols, BMPs, and other
conditions in the plan must, at a minimum,
address the following: manure storage,
mortality management, clean water diversions,
prevention of direct animal contact with water,
chemical handling, conservation practices
to control runoff, manure and soil testing
protocols, land application protocols and record
keeping requirements. 40 CFR § 122.42(e)(1). For
a detailed discussion of each of the minimum
measures, see Chapters 5 and 6.
For Large CAFOs subject to the land application
requirements of the ELG, in addition to the
Discussion is an important part of the permit writing process.
requirements of 40 CFR part 122, the terms of the
(Photo courtesy of USDA/MO NRCS)
NMP must also include the BMPs necessary to
meet the requirements of 40 CFR part 412.4(c).
Part 412.4 requires that the NMP address the form, source, amount, timing and method of
application and include a field-specific assessment of the potential for nitrogen and phosphorus
transport from the field to surface waters. The Director may also allow appropriate flexibilities to
implement nutrient management practices.
Part 122.42(e)(5) further elaborates on the terms of the NMP associated with protocols for land
application. Those must include the fields available for land application, field-specific rates of
application, and any timing limitations on when manure can be land applied. The terms for
rates of application must follow one of two approaches that the regulation identifies as the linear
approach and the narrative rate approach. The terms for each of those approaches are discussed
in detail in Chapter 6 .
While 40 CFR part 122.42(e)(5) specifies the minimum terms of the NMP that must be included
in NPDES CAFO permits, states may adopt additional or more stringent requirements.
CWA section 510.
It is important for permit writers to understand that where the Director incorporates the terms
of a CAFO’s NMP into a general permit, the procedures established in 40 CFR part 122.62 for
permit modification do not apply to CAFO permits. Instead, the regulations include procedures
for incorporation of the terms of the NMP as part of the CAFO general permitting process itself, as
required by 40 CFR part 122.23(h), which establishes the procedures for permit coverage under a
CAFO general permit (see Chapter 3.2).

Including the Terms of the NMP as NPDES Permit Terms
As previously mentioned, the terms of the NMP are the information, protocols, BMPs and
other conditions determined by the Director as necessary to meet the requirements of
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

40 CFR part 122.42(e)(1), and must be included by the permit writer in a CAFO’s NPDES permit
as enforceable terms and conditions of the permit. The terms of the NMP must specify what
the CAFO operator is required to do relating to each of the nine minimum measures when
implementing its NMP and include the specific conditions on which such actions must be based.
There is no requirement concerning where the terms of the NMP must appear in the permit, so
a permit writer has discretion as to how to write the terms into the permit. Because the terms
of the NMP are effluent limits, it is advisable for the permit writer to include all the conditions
associated with the terms of the NMP in a section of the permit dedicated to effluent limitations,
even where the terms are generally applicable to all permitted CAFOs. Where that is done, it is
also a good idea for the permit writer to cross-reference in the site-specific section any generally
applicable conditions of the permit relating to the minimum measures that may be included
elsewhere in the permit.
Given the unique inter-relationship between the NMP and the permit, the permit writer may
choose to establish permit conditions associated with the NMP in a separate part of the permit
from other effluent limitations. For example, in the Example Permit included in this Manual
document, Appendix J, NPDES General Permit Template for CAFOs, multiple sections are
dedicated to effluent limitations; one of which is dedicated to the terms of the NMP.

Establishing the Minimum Measures as NPDES Permit Terms
As discussed in this section and elsewhere in this Manual, depending on the type of permit and
the attributes of the various terms of the NMP, a permit writer may establish the terms of the NMP
as broadly applicable permit conditions that are identical for multiple CAFOs (e.g., all CAFOs
covered by a general permit); as site-specific permit terms based on the facility-specific NMP; or
some combination of both, whereby a broadly applicable permit condition is supplemented with
a site-specific term. Regardless of how the minimum measures are captured as permit terms,
it is important that all permits establish clear and objective requirements. Using site-specific
information from an NMP where available, helps to provide clear and objective requirements for
an operation to satisfy 40 CFR part 122.42(e)(5).
How the permit writer chooses to capture the terms of the NMP in the permit is primarily up to
the permit writer, except to the extent that the CAFO regulations necessitate that certain terms
be site-specific. Moreover, the permit writer’s discretion may be limited by applicable statespecific requirements for certain BMPs. Further, because the public must have an opportunity to
review the NMP and comment on the terms of the NMP to be included in the permit, the extent of
discretion allotted to the permit writer might vary.
Although the permit writer has broad discretion regarding how to write the minimum measures
as permit terms, to facilitate public review of the NMP the permit writer should decide how he
can clearly write the permit terms so that they are easy to locate and are readily understood by
the permitee, permitting authority, and the public. The following section describes different ways
that a permit writer can write permit terms.
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

Terms of the NMP may be written as broadly applicable permit terms for the following mini­mum
measures: mortality management; clean water diversion; prevention of direct animal contact
with water; proper chemical handling; protocols for manure and soil testing; and record-keeping
requirements as long as they provide sufficient clarity for implementation of the terms by the
CAFO. Where broadly applicable terms alone are sufficient to comply with 40 CFR part 122.42(e)(5),
and are established in a general permit, CAFOs may submit NMPs to the Director that do not
duplicate those requirements.
However, when an NMP provides site-specific measures for those terms, the permit writer
should consider whether it is beneficial for clarity to include the site-specific measures to supplement the generally applicable term. As part of that evaluation, the permit writer should also
determine if the NMP is missing any site-specific information that is necessary to comply with
40 CFR part 122.42(e)(5). Where site-specific information is missing, the permitting authority
may require that the CAFO provide supplemental site-specific information for those terms. To the
extent that the CAFO is required to provide supplemental site-specific information in its NMP to
comply with 40 CFR part 122.42(e)(5), that information should be included as part of the terms
of the permit. Examples of both broadly applicable terms and site-specific terms for each of the
minimum measures are in Chapter 5.

Sample permit language for a general permit referencing generally
applicable terms:
The terms of the NMP also include sections [identify section(s)] of this permit concerning
[for example—no direct contact of animals with water of the U.S. or waters that
are discharged to waters of the U.S.; handling and disposal of chemicals and other
contaminants; limitations on the timing of application of manure, litter, and process
wastewater] that are applicable to all CAFOs authorized under this permit and are included
as terms of the NMP for every CAFO covered by this permit.

From time to time, situations can arise where generally applicable permit terms conflict with sitespecific provisions in the NMP. In such instances, the permit writer should include provisions in
the permit that clarifies which of the conflicting (or potentially conflicting) requirements must be
followed by the CAFO when implementing the terms of the NMP.
EPA believes that the requirements for waste storage, 40 CFR part 122.42(e)(1)(i), and conservation
practices to control runoff, 40 CFR part 122.42(e)(1)(vi), have site-specific components; therefore,
it would not be sufficient to write those as generally applicable permit terms. However, because
some elements of those two terms may apply to multiple facilities, EPA encourages permit writers
to write the permit terms for those two measures as a hybrid of broadly applicable permit terms
that are supplemented by site-specific information derived from the permitted CAFO’s NMP.
Examples of those approaches are provided in Chapter 5.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

Sample permit language—generally applicable terms with clarifying language
The terms of the NMP also include [identify section(s)] of this permit concerning [for
example—waste storage and conservation practices to control runoff]. Such terms are
applicable to all CAFOs authorized under this permit, except where the NMP explicitly
includes site-specific alternatives that meet all the requirements of this permit and are
included as terms of the NMP, as follows: [Here list those terms from the NMP to be
incorporated into the permit.]

Finally, the terms of the permit that are conditions that ensure compliance with the requirement
to establish protocols for land application can be written only as site-specific permit terms.
40 CFR § 122.42(e)(5). Those are described in detail in 40 CFR part 122.42(e)(5). The terms for land
application are discussed extensively in Chapter 6.5.

Approaches for Writing Site-Specific Permit Terms of the NMP
When incorporating the site-specific terms of the NMP into the permit, a permit writer may take
a variety of approaches, depending on the type of permit, the complexity and length of the NMP,
and—for rates of application—whether the permittee intends to follow the linear approach or
the narrative rate approach. Those approaches may include (1) incorporation by reference of the
NMP in its entirety; (2) incorporation of only the terms of the NMP by reference, using language
that parallels the regulatory provisions for the terms of the NMP; and (3) a specific, detailed
identification of each of the terms of the NMP in the text of the permit. The discussion that follows
focuses on terms for rates of application but can be used by permit writers when considering how
to incorporate site-specific terms for all the minimum measures.
The first approach for identifying the terms of the NMP in the permit is to incorporate the entire
NMP by reference (blanket incorporation) and attach the NMP to the permit. That would be an
appropriate approach to use when the terms of the NMP are clearly identifiable in the NMP, and
where the NMP does not contain a lot of extraneous information that could be confused with
parts of the NMP that constitute the permit terms. If a permit writer chooses to use that approach,
it is generally not sufficient to merely attach the NMP to the permit. A reference to the attached
NMP and a statement that it is incorporated into the permit is generally necessary to make the
terms of the NMP enforceable as permit conditions. States may have specific legal requirements
or standard text for incorporation by reference.

Sample permit language—blanket incorporation method
The [attached NMP: specify facility, responsible parties, and date of the NMP, as well as
in what manner the NMP is attached to the permit, its location if not physically attached,
etc.] is incorporated by reference and constitutes in its entirety the terms of the NMP,
which are included as terms and conditions of this permit, as determined by the Director
to constitute the information, protocols, BMPs, and other conditions necessary to meet the
requirements of 40 CFR part 122.42(e)(1).

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-26

NPDES Permit Writers’ Manual for CAFOs

For rates of application, this method of incorporation by reference is most suitable where the
permittee is using the linear approach for rates of application, where the only factor of the NMP
that is variable is the amount of manure to be applied. (For a detailed discussion of the linear
approach, see Chapter 6.5.1 and 6.5.2). The conditions that determine the actual amount of
manure to be land applied can be specifically articulated either in the permit or in the NMP itself.
It is not necessary to filter out elements of the NMP that are not actually conditions of the permit,
unless there is a specific concern that there could be confusion as to whether some of the content
of the NMP is considered a term of the NMP. If the concern is limited to only a few issues, this
form of incorporation by reference can be used effectively, as long as clarification is provided.
Incorporation of the NMP in its entirety may also be used where the permittee follows the
narrative rate approach, as long as any factors that can vary during the period of permit coverage
are explicitly discussed in the NMP and the conditions, range, and other appropriate limitations
concerning such variables are clearly described in the NMP. Where a permittee chooses to use the
narrative rate approach, it could be problematic if the permit incorporates the NMP in its entirety,
because the permittee believes that the plan is intended to allow changes to occur at the facility
during the period of permit coverage and that adjustments can be made in the implementation
of the plan, which will be allowed by the permit. If the NMP is incorporated as written, it must be
clear to anyone reviewing the NMP what the terms are that will apply to the CAFO throughout
the period of permit coverage. An NMP incorporated in this fashion will need to specifically
describe the variations that may occur during the period of permit coverage and the conditions
and implications associated with such variations so that changes to the NMP will not require
reopening the plan for review. In those situations, EPA strongly recommends that the NMP itself
clearly describe to the extent possible the array of variables that are anticipated during the period
of permit coverage. Given the complexity of factors associated with rates of application, however,
it might be difficult to specifically identify all the conditions that could vary within the allowable
framework of the narrative rate approach.
When incorporation by reference is done using the blanket incorporation approach, it is important
to keep in mind that the NMP may address more nutrient management practices than are
specifically required by the CAFO regulations. If the permit incorporates the entire NMP by
reference, the permittee will be expected to implement everything as described in the plan, to the
extent that it pertains to the regulatory requirements, whether or not intended by the permit writer.
The second approach by which a permit writer may establish site-specific terms of the NMP in
a permit is through a more detailed form of incorporation by reference. Such a detailed form of
incorporation by reference specifically refers to each portion of the NMP that is incorporated
as a permit term. That would be an appropriate approach to use where the NMP has delineated
sections that relate to the nine minimum measures. Under this approach, it is necessary to ensure
that the permit includes a reference to the NMP and make clear that the terms of the incorporated
NMP are themselves terms and conditions of the permit. See 40 CFR part 122.23(h). Although
it is similar to the blanket incorporation method, this approach has the advantage of providing
some of the nuances identified in the NPDES regulations, thereby avoiding some of the pitfalls of

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-27

NPDES Permit Writers’ Manual for CAFOs

blanket incorporation of the NMP. Of course, changes that exceed the bounds of the narrative rate
approach may be made if the procedures for changes to the NMP are followed (see Changes to a
Permitted CAFO’s NMP, below). The text box below includes sample language for incorporating
the terms for rates of application for a CAFO using the narrative rate approach.

Sample language—incorporation method for rates of application for a CAFO
using the narrative rate approach
The terms of the NMP with respect to rates of application of manure, litter, and process wastewater
include the following:
• The outcome of the field-specific assessment of the potential for nitrogen and phosphorus
transport from each field.
• The crops to be planted in each field or any other uses such as pasture or fallow fields
(including alternative crops identified in accordance with 40 CFR part 122.42(e)(5)(ii)(B).
• The realistic yield goal for each crop or use identified for each field.
• The nitrogen and phosphorus recommendations from sources specified by the Director for
each crop or use identified for each field.
• The methodology by which the NMP accounts for the following factors when calculating the
amounts of manure, litter, and process wastewater to be land applied:
— Results of soil tests conducted in accordance with protocols identified in the NMP, as
required by 40 CFR part 122.42(e)(1)(vii).
— Credits for all nitrogen in the field that will be plant available.
— The amount of nitrogen and phosphorus in the manure, litter, and process wastewater
to be applied.
— Consideration of multiyear phosphorus application.
— Accounting for all other additions of plant-available nitrogen and phosphorus to the field.
— The form and source of manure, litter, and process wastewater.
— The timing and method of land application.
— Volatilization of nitrogen and mineralization of organic nitrogen.
• Alternative crops that are not in the planned crop rotation but that are listed, by field,
where the plan includes the realistic crop yield goals and the nitrogen and phosphorus
recommendations for each such crop.
The following projections in the NMP are not terms of the NMP:
• The planned crop rotations for each field for the period of permit coverage.
• The projected amount of manure, litter, or process wastewater to be applied.
• Projected credits for all nitrogen in the field that will be plant available.
• Consideration of multiyear phosphorus application.
• Accounting for all other additions of plant-available nitrogen and phosphorus to the field.
• The predicted form, source, and method of application of manure, litter, and process
wastewater for each crop.
• Timing of application for each field, as far as it concerns the calculation of rates of application.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

To ensure clarity, in many instances, the best method of incorporating the terms into the permit
might be to specifically delineate the terms of the NMP with site-specific conditions in the permit.
Although that might be resource-intensive from the perspective of the permit writer, it can help to
avoid confusion when the terms of the NMP are established by the permitting authority and when
they are implemented by a CAFO during the period of permit coverage. A permit writer taking
that approach would include all the terms of the NMP in the body of the permit, including all
the terms associated with rates of application. When following that approach, the permit writer
is advised to include a catch-all provision in the permit that ensures that the terms of the NMP
fully encompass all the requirements established in the CAFO regulations. Chapter 6.6 provides
a detailed example of this method for rates of application and illustrates how a permit writer can
identify and extract information from an NMP and use the information to write permit terms for
the protocols for land application minimum measure.
It is worth noting that plan writers can help the permit writer by highlighting the key information
in the plan that identifies the terms of the plan. Similarly, some of that information may be
included in software used in developing the NMP. Permitting authorities may allow plans to rely
on such default information, as long as there is a means of clearly identifying the information
used to develop the NMP and that serves as the basis for the terms of the NMP.
Regardless of the method of incorporation used by the permit writer, it is the permit writer’s
responsibility to ensure that the permit clearly delineates the terms of the NMP so that the CAFO
operator, the public, state and federal inspectors, and others understand what is expected of the
permitted CAFO when it implements its NMP. Some combination of the methods discussed above
may be used to address concerns that might be raised by one or more of the parties when the draft
terms of the NMP are made available for review by the permitting authority. EPA’s expectations
concerning specific terms of the NMP are discussed in detail in Chapters 5 and 6 and are
intended to foster effective permit writing and be helpful in avoiding ambiguities in an NPDES
permit. Chapter 5 includes examples of terminology that may be used for including site-specific
terms for each of the minimum measures in a permit. Chapter 6 includes a detailed example of
terms of the NMP for rates of application.

Changes to a Permitted CAFO’s NMP
Agricultural operations modify their nutrient management and farming practices during the
normal course of their operations. Such alterations might require changes to a permitted CAFO’s
NMP during the period of permit coverage.
Because of the way NMPs are developed and the flexibility provided by the two options for
developing the terms of the NMP at 40 CFR part 122.42(e)(5), most routine changes at a facility
should not require changes to the permit itself. For example, a CAFO using the narrative rate
approach would not ordinarily need to change any permit terms when it makes changes to the
factors that are not themselves terms but are accounted for in the methodology (such as the
timing, method, form, or source of manure to be applied, which are all described in detail in
Chapter 6.5.3). To minimize the need for revision, NMPs should account for and accommodate
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-29

NPDES Permit Writers’ Manual for CAFOs

routine variations inherent in agricultural operations such as anticipated changes in crop
rotation, and changes in numbers of animals and volume of manure resulting from normal
fluctuations or a facility’s planned expansion.
Typically, an NMP is developed to reflect the maximum number of animals confined at the
facility; the maximum capacity for manure storage; the total number of fields available for land
application and their maximum capacity for nutrient applications. Fluctuations under those
maximum amounts would not necessitate changes to NMPs. EPA encourages operators to
develop an NMP that includes reasonably predictable alternatives that a CAFO may implement
during the period of permit coverage. However, unanticipated changes to an NMP and in some
cases, permit terms, might nevertheless be necessary.
The regulation at 40 CFR part 122.42(e)(6)(i) requires a CAFO to notify the Director of changes
to the CAFO’s NMP, and 40 CFR part 122.42(e)(6) excludes the results of calculations made to
calculate the maximum amount of manure. See 40 CFR parts 122.42(e)(5)(i)(B), 122.42(e)(5)(ii)(D).
The results of the calculations, which are required of Large CAFOs using the linear approach and
all CAFOs using the narrative rate approach, must be reported in the CAFO’s annual report. Thus,
there is no need to notify the Director of such types of changes, as long as they are within the
scope of the terms of the NMP applicable to the permitted CAFO.
The regulations at 40 CFR part 122.42(e)(6)(iii) identify a list of changes to the NMP that would
constitute a substantial change to the terms of a facility’s NMP, thus triggering requirements for
public notice and permit modification. Substantial changes include the following:
1. Addition of new land application areas not previously included in the CAFO’s NMP.
2. Any changes to the maximum field-specific annual rates of application or to the
maximum amounts of nitrogen and phosphorus derived from all sources for each crop,
as expressed in accordance with the linear approach or the narrative rate approach.
3. Addition of any crop not included in the terms of the CAFO’s NMP and corresponding
field-specific rates of application.
4. Changes to field-specific components of the CAFO’s NMP, where such changes are likely to
increase the risk of nitrogen and phosphorus transport from the field to waters of the U.S.
The regulations allow a specific exception to the first type of substantial change (a land
application area being added to the NMP), where additional land is already included in the terms
of another existing NMP that is incorporated into an existing NPDES permit. If, under the revised
NMP, the CAFO owner or operator applies manure on the land application area in accordance
with the existing field-specific terms of the existing permit, addition of new land would under the
revised NMP not be a substantial change to the terms of the CAFO owner or operator’s NMP.
The second substantial change is any change to the field-specific maximum rates of application.
The regulations clarify that, for the narrative rate approach, a substantial change is triggered by a
change in the field-specific maximum amount of nitrogen and phosphorus derived from all sources.
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-30

NPDES Permit Writers’ Manual for CAFOs

District Conservationist reviewing a conservation plan with a
farmer in Orange County, Virginia.
(Photo courtesy of USDA/NRCS)

The third substantial change is the addition to
the NMP of crops or other uses not previously
included in the CAFO’s NMP, together with the
corresponding maximum field-specific rates
of application for those crops or other uses.
Because rates of application are based on the
yield goals for each specific crop, any crops
or other uses that are added to the plan will
require corresponding newly calculated rates of
application. In addition, because the maximum
rates of application must be made available to
the public for review before incorporation as
terms of the permit, the addition of new crops
or other uses and their corresponding rates of
application is considered a substantial change.

Finally, any change to site-specific components
of the CAFO’s NMP that is likely to increase
the risk of nitrogen and phosphorus transport to waters of the U.S. is a substantial change. The
actual crop planted, timing and method of land application, and conservation practices used
with respect to the land application areas are all key factors that affect nitrogen and phosphorus
runoff from the land application area. Changes to any of the planning considerations listed above
can alter the outcome of the decisions made in an NMP and the efficacy of that plan in ensuring
appropriate agricultural utilization of those nutrients that are land applied.

Whether a change to any of those factors would be considered a substantial change for purposes
of 40 CFR part 122.42(e)(6)(iii) is linked to the outcome of the field-specific risk assessment, which is
a permit term for both the linear and narrative rate approaches. The outcome of the field-specific
risk assessment evaluates the risk of nutrient runoff from a field to surface waters, and establishes
the baseline risk parameters for both nitrogen and phosphorus. Chapter 6.5.1 discusses that
permit term in detail.
The risk of nitrogen runoff is minimized as long as a crop’s nitrogen need is not exceeded and
as long as the crops’ nitrogen need is based on the realistic crop yield goal and all contributing
credits of available nitrogen. This permit term is crop specific, so any changes to the crop such as
a change in the yield goal or a change in the type of crop would change the amount of nitrogen
that would be land applied. The risk of nitrogen transport increases when the amount of nitrogen
that is applied exceeds the amount identified in the permit for the planned crops. That increase in
risk would result in a substantial permit change under 40 CFR part 122.42(e)(6)(iii).
There are various methods for assessing the risk of phosphorus transport from fields, such as soil
test, soil phosphorus threshold, and the phosphorus index. As discussed in Chapter 6.5.1, the
method for assessing the risk of phosphorus transport should be identified in a state’s technical
standard, and the outcome of the assessment is the permit term. The linear and narrative
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-31

NPDES Permit Writers’ Manual for CAFOs

rate approaches for writing this permit term affect whether a change in risk would rise to be a
substantial change under 40 CFR part 122.42(e)(6)(iii). (For further discussion, see Chapter 6.5.4.)
The four substantial changes identified in the regulations are applicable to both the linear and
narrative rate approaches for expressing rates of application. For example, proper implementation
of the narrative rate approach depends on identifying the fields to be used for land application,
so use of a new field for land application that had not been previously covered in the facility’s
(or another facility’s) permit terms would constitute a substantial change. In addition, under
the narrative rate approach, a change to the field-specific maximum amounts of nitrogen and
phosphorus derived from all sources is a substantial change to the NMP because it defines the
upper bounds on nutrient additions.
Finally, NPDES permits for all types of dischargers, including CAFOs, typically include reopener
provisions under which the Director may revise the permit during the permit term on the
basis of factors such as changes to the status of the receiving waterbody. Such standard NPDES
provisions are sufficient to allow permit revisions necessary to support the criteria and standards
established for receiving waters.
An advantage of the narrative rate approach is that it reduces the likelihood that changes to
a CAFO’s operation would result in a substantial change to the terms of the CAFO’s NMP. For
example, a change to the method or timing of application would be a substantial change to the
terms of the NMP for CAFOs using the linear approach if the Director determines that it is likely
to increase the risk of nutrient transport to surface waters. For a CAFO using the narrative rate
approach, a change in the method or timing of application would not be a change to the terms of
the NMP, and therefore not a substantial change, as long as the methodology in the NMP (itself a
permit term) accounts for the change in method or timing.
Because changes to the NMP could result in a change to a permit term, the owner or operator is
required to provide the Director with the revised NMP and identify the changes from the previous
version submitted. Of course, any change to the CAFO’s implementation of its NMP that does not
constitute a change to the NMP itself would not be submitted to the Director. For example, for
CAFOs following the narrative rate approach, any change in crop rotation or substitution of crops
in a given rotation with alternative crops identified in the NMP for a given field would not be a
change and, thus, would not need to be submitted to the Director before implementation.

Process for Review and Modification of the NMP
When a permitted CAFO operator revises its NMP, the CAFO regulations require the owner or
operator to submit the revised NMP to the permitting authority for review and for the permitting
authority to incorporate any revised terms of the NMP into the permit. The regulation at 40 CFR
part 122.42(e)(6) includes provisions that enable the Director to determine whether revisions to
the CAFO’s NMP necessitate revisions to the terms of the NMP incorporated into the permit,
and if so, whether such changes are substantial or nonsubstantial. Figures 4-1 and 4-2 illustrate
the NMP review process as well as necessary steps for determining and making revisions to the
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

Figure 4-1. Process for Review and
Modification of the Nutrient Management
Plan

Figure 4-2. Process for Review and Modification of the
Nutrient Management Plan (detail)

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-33

NPDES Permit Writers’ Manual for CAFOs

permit terms. The regulation identifies several specific types of changes that must be considered
substantial changes to the NMP It also establishes a streamlined process for formal public notice
and comment that the permitting authority must follow for permit modification when a CAFO
is seeking to make substantial changes to the terms of its NMP. Nonsubstantial changes to the
terms of the NMP are not subject to public notice and comment before the permit is revised.
Those procedures apply to all permitted CAFOs, regardless of whether they are covered under an
individual permit or under a general permit.
When a Director receives a revised plan, 40 CFR part 122.24(e)(6)(ii) requires the Director to then
review the revised plan to ensure that it still meets the requirements of 40 CFR part 122.42(e)
and applicable effluent limitations and standards, including those specified in 40 CFR part 412.
The Director must also determine whether the changes necessitate revision to the terms of the
NMP that were incorporated into the permit issued to the CAFO. If not, the Director must notify
the CAFO that the permit does not need to be modified. On such notification, the CAFO may
implement the revised NMP.
If, on the other hand, the Director determines that the changes to the NMP do require that
the terms of the NMP that were incorporated into the permit be revised, the Director must
next decide whether the change is substantial. The Director must evaluate the change on
the basis of the provisions in 40 CFR part 122.42(e)(6)(iii) discussed above. Pursuant to
40 CFR part 122.42(e)(6)(ii)(A), for nonsubstantial changes, the Director must make the revised
NMP publicly available and include it in the permit record, revise the terms of the NMP
incorporated into the permit, and notify the owner or operator and inform the public of any
changes to the terms of the NMP that are incorporated into the permit. On such notification the
CAFO, may implement the revised NMP.
If the changes to the terms of the NMP are substantial, the regulations provide for a public review
and comment period before the Director modifies the permit by incorporating revised terms of
the NMP. 40 CFR § 122.42(e)(6)(ii)(B). The process for public comments, hearing requests, and the
hearing process if a hearing is granted must follow the procedures for draft permits set forth in
40 CFR parts 124.11–124.13. The Director must respond to all significant comments received during
the comment period as provided in 40 CFR part 124.17 and require the CAFO owner or operator to
further revise the NMP if necessary. Once the Director incorporates the revised terms of the NMP
into the permit, the Director must notify the owner or operator and inform the public. Such a type
of permit modification may be appealed in the same manner as the initial, final permit decision.
The Director may establish by regulation or in the general permit for CAFOs an appropriate
period that differs from the period specified in 40 CFR part 124.10 for the public to comment and
request a hearing on the proposed substantial changes to the terms of the NMP incorporated into
the permit. Allowing the Director to establish a different period from 40 CFR part 124.10 provides
the Director the discretion to allow CAFOs to implement revised nutrient management practices
in accordance with growing seasons and other time-sensitive circumstances. When proposing
the period that differs from 40 CFR part 124.10, the public must have an opportunity to comment
on the sufficiency of the proposed period.
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards
4.1.7. Nutrient Management Plan (NMP)

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

Because the process in 40 CFR part 122.42(e)(6)(ii) allows for public review of substantial changes
to the terms of NMPs and the underlying data and calculations, the incorporation of changes to
the permit through the process is a minor permit modification under 40 CFR part 122.63(h), and
no additional review of the permit modification is required.
The process and timing of modifying a permit will vary. A CAFO owner or operator must remain
in compliance with his or her permit and, thus, should work closely with the permitting authority
and should initiate the coordination as early as possible.
The regulations do not provide a permitting authority with the discretion to preapprove certain
substantial changes, unless they are specified in an NMP that encompasses normal fluctuations
or variations. That is because the Waterkeeper decision held that the terms of the NMPs must be
subject to permitting authority review and be available for public comment.

4.1.8. Agricultural Stormwater Exemption for Permitted CAFOs
All permits issued to CAFOs that land apply manure must contain terms and conditions that,
when implemented, ensure that all precipitation-related discharges from land application are
composed entirely of agricultural stormwater. Section 502(14) of the CWA excludes from the
definition of a point source agricultural stormwater discharges. The CAFO regulations establish
when a discharge from a land application area under the control of a CAFO is considered to
be exempt agricultural stormwater, as opposed to a point source discharge from the CAFO.5 A
precipitation-related discharge from a CAFO’s land application areas is considered agricultural
stormwater only when the manure was applied in accordance with site-specific nutrient
management practices that “ensure appropriate agricultural utilization of the nutrients” in the
manure to be applied. 40 CFR § 122.23(e). For CAFOs, the agricultural stormwater exemption
applies only to discharges from land application areas.6 Furthermore, discharges occurring
during dry weather can never be discharges of agricultural stormwater.
Criteria for site-specific nutrient management practices for land application are specified in
40 CFR parts 122.42(e)(1)(vi)-(ix). Those are discussed in greater detail in Chapter 6. For per­
mitted CAFOs, the permit must set forth the, “site-specific nutrient management practices”
that will be implemented for each requirement of 40 CFR parts 122.42(e)(1)(vi)-(ix). Under
40 CFR part 122.42(e)(1)(vii), all permitted CAFOs must establish field-specific application
rates for manure. The site-specific land application rates must be established as enforce­
able terms in the facility’s NPDES permit following either the linear approach described in
40 CFR part 122.42(e)(5)(i), or the narrative rate approach described in 40 CFR part 122.42(e)(5)(ii)
(see Section 6.5).

Permitted Large CAFOs
In addition to the requirements described above, permitted Large CAFOs subject to the require­
ments of subpart C and D of Part 412 must also meet the requirement of 40 CFR part 412.4(c) to
qualify for the agricultural stormwater exemption. 40 CFR §§ 122.23(e)(1), 122.42(e)(1). The ELG
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.8. Agricultural Stormwater Exemption for Permitted CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

specifies requirements for implementing
site-specific application rates, manure and
soil sampling, and setback requirements.
Additionally, it provides protocols for
inspecting the land application equipment.
See discussion in Section 4.1.3.
The site-specific application rates for
manure must be developed in accordance
with technical standards established by the
Director. 40 CFR § 412.4(c)(2). The rates must
also be identified in the facility’s NPDES
permit as enforceable terms following either
the linear approach or narrative rate approach
(73 FR 70420). The technical standards
are discussed in Chapter 6.3.1, and sitespecific rates of application are discussed in
Chapter 6.5.

Precipitation related runoff from a land application area
where manure has been applied in accordance with an NMP
is exempt as agricultural stormwater.
(Photo courtesy of USDA/NRCS)

Permitted Small and Medium CAFOs
For precipitation-related discharges from the land application area of a Medium or Small
CAFO to qualify for the agricultural stormwater exemption, the owner or operator of the
CAFO must implement an NMP that includes the practices and protocols specified in
40 CFR part 122.42(e)(1)(vii)-(ix).
Effluent limitations for Medium and Small CAFOs are based on the BPJ of the permit writer. As
discussed in Section 4.1.4, permit writers could find that it is appropriate to develop BPJ effluent
limitations that are the same as, or similar to, the effluent limitations established in the ELG
for Large CAFOs. Thus, a Medium or Small CAFO might be required to develop protocols for
land application in accordance with the state technical standards for nutrient management and
comply with the requirement for a 100-foot setback or a 35-foot vegetated buffer between land
application areas and any downgradient surface waters or conduits to surface waters. Because the
practices for ensuring appropriate agricultural utilization of the nutrients in land-applied manure
at Large CAFOs do not differ significantly for Medium and Small CAFOs, the permit writer might
find it appropriate to apply the requirements established in the state technical standards equally
to land application sites at all permitted CAFOs.

4.1.9. Water Quality-Based Effluent Limitations and Standards
As discussed in Section 4.1.1, all NPDES permits must include technology-based effluent limita­
tions. However, a permit must also include more stringent water quality-based limitations when
such limitations are necessary to meet water quality standards. CWA sections 402(a), 301(b)(1)(C).

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.9. Water Quality-Based Effluent Limitations and Standards

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

A water quality-based effluent limitation is designed to ensure that state or tribal water quality
standards are met. Federal regulations require permit limitations to control all pollutants
that could be discharged at a level that will cause, have the reasonable potential to cause, or
contribute to an excursion above any state water quality standard. 40 CFR §§ 122.4(d), 122.44(d).
That includes, where appropriate, water quality-based effluent limitations for the production area,
land application area, and all other discharges covered by the permit.

Requirements for the Production Area of Large CAFOs
The permit writer may determine the need to establish more restrictive requirements for the
production area. Even for CAFOs subject to a no-discharge, technology-based standard for the
production area, situations could arise where the permitting authority needs to impose more
stringent requirement for allowable discharges. Specifically, more stringent discharge limitations
are necessary in instances where CAFOs discharge from a production area to a waterbody listed
under CWA section 303(d) as impaired due to nutrients, dissolved oxygen or bacteria, or where
an analysis of frequency, duration and magnitude of the anticipated discharge (consisting of
potential overflows of manure, litter, or process wastewater) indicates the reasonable potential to
violate applicable water quality standards.
The imposition of a water quality-based effluent limitation could necessitate a more stringent
standard or the inclusion of additional management practices. Examples of such practices
include additional storage capacity beyond that required by technology-based limits, monitoring
the water quality of the waterbody and monitoring the extent of impairment where a discharge
occurs, and installing an impermeable lining in a lagoon or storage pond.

Requirements for the Land Application Area of Large CAFOs
As discussed in Section 4.1.7, all permitted CAFOs are required to develop and implement an
NMP. When a permitted CAFO implements an NMP in accordance with its permit requirements,
any remaining precipitation related discharges of manure are considered agricultural
stormwater, as discussed in Section 4.1.8. For Large CAFOs subject to the ELG, that also means
that the NMP must comply with permit requirements that implement the ELG, including
technical standards established by the Director for nutrient management. For facilities not
subject to the ELG, it means that the NMP must comply with permit requirements that implement
40 CFR part 122.42(e) and any additional nutrient management requirements developed by BPJ.
As previously mentioned, by definition, the agricultural stormwater exemption applies only to
precipitation-related discharges. Any other discharges from the land application area allowed by
the permit may be subject to more stringent water-quality based requirements (unless they are
exempted irrigation return flows), as appropriate, to protect water quality. Those may be included
in the permit as water-quality based effluent limits. They might also be addressed through the
development of more protective technical standards for land application.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.1.9. Water Quality-Based Effluent Limitations and Standards

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-37

NPDES Permit Writers’ Manual for CAFOs

In addition, where there are water quality impacts associated with precipitation-related
discharges from CAFO land application areas, permitting authorities are encouraged to update
their technical standards to include requirements that are more protective of water quality.
68 FR 7,198 (Feb. 12, 2003).
Appropriate land application practices might include requiring phosphorus-based application
rates for all manure application, additional timing restrictions such as prohibiting manure
application on frozen ground, additional mandatory setbacks or buffers, groundwater monitoring
requirements, or prohibiting multiyear application of phosphorus.

4.2. Monitoring, Record-Keeping, and Reporting
Requirements of NPDES Permits for CAFOs
The NPDES regulations identify record-keeping, monitoring, and reporting requirements that
are applicable to all CAFOs. 40 CFR §§ 122.41, 122.42(e)(2)-(4). The CAFO ELG identify additional
record-keeping and monitoring requirements that are applicable only to Large CAFOs. The
record-keeping requirements associated with the off-site transfer of manure are applicable to
Large CAFOs. For CAFOs not subject to the ELG, additional monitoring and record-keeping
requirements may be established as technology-based limits by the permitting authority on a
case-by-case basis using BPJ (see Section 4.1.4).

4.2.1. Monitoring Requirements
When developing the monitoring requirements for NPDES permits, the permit writer should
address the routine operational characteristics of the facility and the minimum reporting
requirements at 40 CFR part 122.41(l). The ELG includes specific monitoring requirements
for daily and weekly visual inspections of
specific aspects of the production area and
monitoring requirements associated with land
application, including manure and soil analysis
and land application equipment inspection.
40 CFR §§ 412.37, 412.47. Although the ELG
requirements apply only to Large CAFOs
subject to Part 412 subparts C and D, the permit
writer should consider those as a starting point
when establishing BPJ requirements for other
permitted CAFOs. The permit should also
include monitoring requirements that address
nonroutine activities. For example, discharges
at a CAFO can occur because of an overflow
during a catastrophic storm event (which may
Sampling of wastewater from a lagoon on a hog farm.
be an allowable discharge under the terms
(Photo courtesy of USDA/NRCS)
of the permit) or a leak, breach, overflow, or
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs
4.2.1. Monitoring Requirements

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-38

NPDES Permit Writers’ Manual for CAFOs

other structural failure of a storage facility because of improper operation, design, or maintenance
(which would be an unauthorized discharge). Unauthorized discharges could also occur because
of manure releases related to the improper storage or handling of liquid or solid manure, or
improper land application. The permit must require specific data collection activities (as well
as notification and reporting activities as described in Section 4.2.3, Reporting Requirements).
40 CFR § 122.41(l)(6). As explained in Section 4.1.8 where there is a discharge from the production
area to an impaired water, a permit writer may impose more restrictive water quality-based
effluent limitations that could include additional monitoring requirements.
The monitoring requirements include an analysis of the discharge, if needed to determine com­
pliance by the permitting authority. 40 CFR § 122.44(g). At a minimum, the analysis should
include total nitrogen, ammonia nitrogen, P, pH, temperature, Escherichia coli or fecal coliform,
5-day bio­chemical oxygen demand (BOD5), and total suspended solids. 40 CFR § 122.44(g). The
analysis is to be performed in accordance with approved EPA methods for wastewater analysis
listed in 40 CFR part 136. The permitting authority might wish to specify additional parameters at
its discretion.

4.2.2. Recordkeeping Requirements
CAFO operators should maintain in their records a copy of the current NPDES permit and any
supplemental documents identified by the permitting authority. Permits should specify that all
CAFOs must retain copies of all required documentation. In addition, permits should require
that the records be organized in a manner that inspectors can easily review during a compliance
inspection, such as the use of a dedicated logbook. The required records for Large CAFOs are
listed in Table 4-6 and for Small and Medium CAFOs in Table 4-7. Records must be maintained for
5 years.

Recordkeeping is an important part of the permitting process.
(Photo courtesy of USDA/ARS)

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs
4.2.2. Recordkeeping Requirements

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-39

NPDES Permit Writers’ Manual for CAFOs

Table 4-6. Required records for permitted Large CAFOs
Regulatory requirement for
recordkeeping

Records required

Requirements to maintain records for the nine minimum terms of the NMP.
40 CFR § 122.42(e)(2)
Adequate storage capacity

Satisfied by requirements of 40 CFR part 412.37(b) (below)

Mortality management

Satisfied by requirements of 40 CFR part 412.37(b) (below)

Divert clean water

Satisfied by requirements of 40 CFR part 412.37(b) (below)

Prevent direct contact with waters of
U.S.

Identify what waters of the U.S., if any, exist within the
animal confinement areas and the measures, including
operation, and maintenance procedures and associated
records, that are implemented to prevent animals from
contacting waters of the U.S.

Chemical disposal

Identify chemicals used or stored (or both) on-site and
document appropriate disposal methods

Conservation practices to control
runoff to waters of the U.S.

Identify the conservation practices used to control
pollutant runoff, including location, and the protocols
and procedures, including installation, operation,
and maintenance, and associated records, that are
implemented to ensure the practices function to control
pollutant runoff

Manure and soil testing

Satisfied by requirements of 40 CFR part 412.37(c) (below)

Protocols for land application

Satisfied by requirement of 40 CFR parts 122.42(e)(2)(ii)
and 412.37(c) requirement to maintain on-site a sitespecific NMP

Requirements to maintain records for the production area. 40 CFR § 412.37(b)
A complete copy of the information
required by 40 CFR part 122.21(i)(1)

The name and owner or operator
The facility location and mailing address
Latitude and longitude of the entrance of the production
area
A topographic map of the geographic area in which the
CAFO is located showing the location of the production
area
Specific information about the number and type of
animals
Type of confinement animals are in (open confinement or
housed under a roof)

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs
4.2.2. Recordkeeping Requirements

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-40

NPDES Permit Writers’ Manual for CAFOs

Table 4-6. Required records for permitted Large CAFOs (continued)
Regulatory requirement for
recordkeeping
A complete copy of the information
required by 40 CFR part 122.21(i)(1)
(continued)

Records required
The type of containment and storage (anaerobic lagoon,
roofed storage shed, storage ponds, under floor pits,
aboveground storage tanks, belowground storage tanks,
concrete pad, impervious soil pad, other)
The total capacity for manure, litter, and process
wastewater storage (tons/gallons)
The total number of acres under control of the applicant
available for land application of manure, litter, or process
wastewater
Estimated amounts of manure, litter, and process
wastewater generated per year (tons/gallons)
Estimated amounts of manure, litter, and process
wastewater transferred to other persons per year
(tons/gallons)
The site-specific NMP

Requirements to maintain records for the production area. 40 CFR § 412.37(b)
Records documenting the inspections
40 CFR § 412.37(a)(1)

Necessary documentation for inspections of the
production area
Records documenting weekly inspections of all
stormwater diversion devices, runoff diversion
structures, and devices channeling contaminated
stormwater to the wastewater and manure storage and
containment structure
Records documenting daily inspection of water lines,
including drinking water or cooling water lines
Records documenting weekly inspections of the manure,
litter, and process wastewater impoundments

Wastewater levels
40 CFR § 412.37(b)(2)

Weekly records of the manure and wastewater level in
liquid impoundments as indicated by the required depth
marker

Corrective actions
40 CFR § 412.37(b)(3)

Records of any actions taken to correct deficiencies found
in the visual inspections of the production area
An explanation of the factors preventing immediate
correction of any deficiencies identified in the visual
inspections of the production area that are not corrected
within 30 days

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs
4.2.2. Recordkeeping Requirements

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-41

NPDES Permit Writers’ Manual for CAFOs

Table 4-6. Required records for permitted Large CAFOs (continued)
Regulatory requirement for
recordkeeping

Records required

Mortality management required
40 CFR §§ 412.37(b)(4), (a)(4)

Records must identify that mortalities were not disposed
of in any liquid manure or process wastewater system.
They must also identify that mortalities were handled in
such a way as to prevent the discharge of pollutants to
surface water, unless alternative technologies pursuant to
40 CFR part 412.31(a)(2) and approved by the Director are
designed to handle mortalities.

Storage structure design
40 CFR § 412.37(b)(5)

Current design of any manure or litter storage structures,
including volume for solids accumulation, design
treatment volume, total design volume, and approximate
number of days of storage capacity

Overflows
40 CFR § 412.37(b)(6)

The date, time, and estimated volume of any overflow

Requirements to maintain records for the land application area. 40 CFR § 412.37(c)
Expected crop yields
Weather conditions 24 hours before application, at time of
application, and 24 hours after application
Explanation of the basis for determining manure
application rates, as provided in the technical standards
established by the Director
Calculations showing the total nitrogen and phosphorus
to be applied to each field, including sources other than
manure, litter, or process wastewater
Total amount of nitrogen and phosphorus actually applied
to each field, including documentation of calculations for
the total amount applied
The method used to apply the manure, litter, or process
wastewater
Test methods used to sample and analyze manure, litter,
process wastewater, and soil. 40 CFR §§ 412.37(c), 47(c)
Results from manure, litter, process wastewater, and soil
sampling. 40 CFR § 412.37(c)
Date(s) of manure application equipment inspection
Additional recordkeeping
requirements

Records required

40 CFR § 412.37(c)

At the discretion of the permitting authority

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs
4.2.2. Recordkeeping Requirements

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4-42

NPDES Permit Writers’ Manual for CAFOs

For Medium and Small CAFOs, the monitoring and record-keeping requirement for the effluent
limitations are established by the permitting authority on a case-by-case basis. The inclusion of
additional record-keeping requirements in the permit for Large CAFOs would be at the discretion
of the permitting authority. The specific record-keeping requirements for other CAFOs would be
established by the permitting authority.
Table 4-7. Required records for permitted Small and Medium CAFOs
Regulatory requirement for
recordkeeping

Responsive records or documentation

Requirements to maintain records for nine minimum terms of the NMP.
40 CFR §122.42(e)(1)(ix)
Adequate storage capacity

Documentation of the storage capacity required to meet
permit requirements and the storage capacity available

Mortality management

Records of practices implemented to meet the mortality
disposal or management practices (or both) of the permit

Divert clean water

Document implementation of any operation and
maintenance practices used to ensure that clean water is
diverted as appropriate

Prevent direct contact with waters
of the U.S.

Identify what waters of the U.S., if any, exist within the
animal confinement areas and the measures, including
operation and maintenance procedures and associated
records, that are implemented to prevent animals from
contacting waters of the U.S.

Chemical disposal

Identify chemicals used or stored (or both) on-site and
document appropriate disposal methods

Conservation practices to control
runoff to waters of the U.S.

Identify the conservation practices used to control
pollutant runoff, including location, and the protocols
and procedures, including installation, operation, and
maintenance, and associated records, that are implemented
to ensure the practices function to control pollutant runoff

Manure and soil testing

Results of manure and soil tests taken to meet the
requirements of the permit and NMP

Protocols for land application

Satisfied by requirement of 40 CFR part 122.42(e)(2)(ii)
requirement to maintain on-site a site-specific NMP

Additional record-keeping requirement to satisfy the effluent limitations
Determined by the permitting authority on a case-by-case basis

Appendix D, Example Nutrient Management Plan Record Keeping Forms, and Appendix M,
Nutrient Management Recordkeeping Calendar, include some examples of record-keeping forms.
Those forms can help the operation meet some of the record-keeping requirements specified in
the regulations.
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs
4.2.2. Recordkeeping Requirements

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

4.2.3. Reporting Requirements
Reporting requirements are generally linked to monitoring requirements and can include
periodic reports, emergency reports for overflow events, and special reports. When developing
the reporting requirements for an NPDES permit, the permit writer should consider monitoring
requirements for routine operational characteristics of the facility, including the required annual
report, and the minimum reporting requirements at 40 CFR part 122.41(l). The permit also should
include reporting requirements that address nonroutine activities such as discharge notification
(for both authorized and unauthorized discharges). The permit must require immediate
notification of the permitting authority and a follow-up report describing the specific data
collection activities required for discharges. 40 CFR § 122.41(l)(6). The reporting requirements
must ensure that the permittee provides a description of the discharge, describes the time and
duration of the event, identifies the cause(s) of the discharge, and provides the result of any
required an analysis(es) to the permitting authority. 40 CFR §§ 122.41(l)(6), 122.44(g).

Annual Reports
All NPDES permits for CAFOs must include a requirement
that the permittee submit an annual report with specific
information defined in the regulation. 40 CFR § 122.42(e)(4).
In addition to the information required by the NPDES
regulations, state permitting authorities can require
additional information to be included with the annual
report. As with NOIs, EPA will promote electronic
submission of annual reports and immediate posting
on publicly available locations. Appendix C, Example
NPDES CAFO Permit Annual Report Form includes all the
information specified in the NPDES CAFO regulation.
The annual report must include the following.
40 CFR § 122.42(e)(4)
▶ The number and type of animals confined at the
CAFO.
▶ Estimated total amount of manure, litter, and process wastewater generated by the
CAFO in the previous 12 months (tons/gallons).
▶ Estimated total amount of manure, litter, and process wastewater transferred to other
persons by the CAFO in the previous 12 months (tons/gallons).
▶ Total number of acres for land application covered by the NMP.
▶ Total number of acres under control of the CAFO that were used for land application of
manure, litter, and process wastewater in the previous 12 months.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs
4.2.3. Reporting Requirements

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

▶ Summary of all manure, litter, and process wastewater discharges from the production
area that have occurred in the previous 12 months, including the date, time, and
approximate volume of the discharge.
▶ A statement indicating whether the current version of the CAFO’s NMP was developed
or approved by a certified nutrient management planner.
▶ The actual crop(s) planted and actual yield(s) for each field.
▶ The nitrogen and phosphorus content of the manure, litter, and process wastewater
as reported on the laboratory report for the required analyses (lbs/ton, g/Kg,
pounds/1,000 gallons, mg/L, ppm).
▶ The results of calculations conducted in accordance with the approved NMP to
determine the amount of manure, litter, or process wastewater to apply.
▶ The amount of manure, litter, and process wastewater applied to each field during the
previous 12 months.
▶ For any CAFO that implements an NMP that addresses rates of application in
accordance with the narrative rate approach:
•

The results of any soil testing for nitrogen and phosphorus conducted during the
previous 12 months.

•

The data used in calculations conducted in accordance with the methodology in
the approved NMP to determine rates of nitrogen and phosphorus application
from manure, litter, and process wastewater.

• The amount of any supplemental fertilizer applied during the previous 12 months.
Part 122.42(e)(4)(viii) requires all permitted CAFOs to include in their annual reports the actual
crop(s) planted and actual yield(s) for each field, the actual nitrogen and phosphorus content
of the manure, litter, and process wastewater, and the amount of manure, litter, or process
wastewater applied to each field during the previous 12 months. It is important for the permitting
authority to obtain that information annually to ensure that the CAFO has been operating in
compliance with the terms of its permit. The annual report will inform the Director and the
public how the CAFO has operated, given the flexibility for the terms of the NMP incorporated
into the permit.
CAFOs that follow the narrative rate approach for describing rates of application in the NMP must
also submit as part of their annual report the results of all soil testing and concurrent calculations
to account for residual nitrogen and phosphorus in the soil, all recalculations, and the new data
from which they are derived. 40 CFR § 122.42(e)(5)(ii). The CAFO is required to report the amounts
of manure and the amount of chemical fertilizer applied to each field during the preceding
12 months. Together with the total amount of plant-available nitrogen and phosphorus from
all sources, the information that is required to be included in the annual report provides the
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs
4.2.3. Reporting Requirements

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

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NPDES Permit Writers’ Manual for CAFOs

information necessary to determine that the CAFO was adhering to the terms of its permit when
calculating amounts of manure to apply.
The narrative rate approach requires the CAFO to recalculate the projected amount of manure, to
be land applied, using the methodology in the NMP, at least once a year, throughout the period of
permit coverage. 40 CFR § 122.42(e)(5)(ii). To ensure that such recalculations are made available
to the Director and the public, the recalculations and the new data from which they are derived
are required to be reported in the CAFO’s annual report, in which the recalculations and data for
the previous 12 months must be reported.
The annual report requirements are for use only in addressing implementation of existing NMP
provisions and changes to the NMP contemplated through flexibilities built into the NMP during
the initial planning process or later modifications in accordance with 40 CFR part 122.42(e)(6).
Because the terms of the NMP are incorporated as enforceable terms and conditions of the
permit, any change that results in a change to the terms of the NMP constitutes a change to the
permit and therefore must be processed in accordance with 40 CFR part 122.42(e)(6).

4.3. Special Conditions for All NPDES Permits for CAFOs
The NPDES regulations require every CAFO permittee to maintain permit coverage until the
CAFO no longer discharges or is properly closed. 40 CFR § 122.22(g). In addition, NPDES permits
issued to Large CAFOs must include a special condition that requires the operator to collect and
maintain information concerning the transfer of manure to other persons (see Section 4.3.3).
Permitting authorities have the discretion to add special conditions to NPDES permits to address
site-specific conditions at the CAFO to minimize the discharge of nutrients to waters of the U.S.
40 CFR § 122.44(k).

4.3.1. Additional Special Conditions as Determined by the
Permitting Authority
NPDES permits for CAFOs may include additional special conditions as determined necessary by
the permitting authority.
The permitting authority has the discretion to include additional special conditions in NPDES
permits for CAFOs beyond those required by the NPDES CAFO regulations where it has
determined that they are necessary to achieve effluent limitations and standards under the
CWA. 40 CFR § 22.44(k). For example, such additional requirements could address emergency
discharge impact abatement, extended storage periods, irrigation control, spills, discharges
from field drain tiles, measurement of rainfall, protection for endangered species and migratory
birds, employee training, and groundwater that has a direct hydrologic connection to waters of
the U.S. In addition, states concerned with groundwater may require monitoring, liners, or other
requirements in accordance with appropriate state authority. CWA § 510.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4.3.1. Additional Special Conditions as Determined by the Permitting Authority

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NPDES Permit Writers’ Manual for CAFOs

4.3.2. Duty to Maintain Permit Coverage until the CAFO
is Properly Closed
Under the revised regulations, permit coverage must be maintained until the facility has
ceased operation or is no longer a CAFO or that the facility no longer discharges manure that
was generated while the operation was a CAFO, other than agricultural stormwater from land
application areas. 40 CFR § 122.23(g).
Once an operation is issued an NPDES permit, that permit remains in place for the entire life
of the permit term, independent of the specific number of animals confined at any time. For
example, a beef operation with 1,200 cattle meets the definition of a Large CAFO and is subject to
regulation. It applies for and is issued an NPDES permit. After issuance of the permit, 400 cows
are transported off the operation, leaving 800 cattle at the operation. The permit remains in
place, and the operation must continue to comply with its requirements. If the operation has
taken the steps to permanently reduce the number of animals confined to a number less than
the regulatory threshold and it would not meet the definition of a Medium CAFO, it can request
that the permitting authority terminate the permit, as long as the operation no longer discharges
manure that was generated while the facility was operated as a CAFO.

Closure Documentation

The sun goes down over a farm.
(Photo courtesy of USDA/NRCS)

Specific information to be submitted to document proper
closure would be established at the discretion of the
permitting authority. Because of the variation in site
management practices, it is unlikely that there will be a
standard package of documentation that addresses whether
an operation has been properly closed or no longer meets
the definition of a CAFO and has no potential to discharge
to waters of the U.S. any manure generated while it was
a CAFO. The key information to be submitted by the
permittee to document such change should focus on that
which establishes a permanent change to the number of
animals held in confinement and the necessary changes to
the manure and wastewater storage and use practices. In
those cases where a permitted CAFO has ceased operation,
the documentation may include records of sale for the
animals confined specifying the date at which no animals
remained in confinement. In addition, the land application
or transfer records should document the disposition of all
the manure and wastewater associated with those animals,
either in accordance with a site-specific NMP or transferred
off-site, for the period up to and including the date at which
the operation no longer met the definition of a CAFO.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4.3.2. Duty to Maintain Permit Coverage until the CAFO is Properly Closed

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NPDES Permit Writers’ Manual for CAFOs

That information could include the submission of a certification, prepared by a professional
engineer licensed in the state, that any liquid storage structure has been properly closed and
that pollutants associated with manure will not migrate from the closed structure to waters of
the U.S. Permitting authorities should also be aware that NRCS has established a Conservation
Practice Standard addressing the closure of such facilities. The standard is titled Closure of Waste
Impoundments and is identified as Practice Code 360.
In cases where a permitted CAFO claims that it
no longer meets the definition of a CAFO or has
addressed the factors that resulted in its being
designated as a CAFO, the permitting authority
should request information that documents the
permanent reduction in the number of animals
confined and that the amount of wastewater being
generated and stored at the operation is consistent
with the reduction. Permitting authorities might
wish to conduct an inspection of the operation
to confirm that it has been properly closed. With
respect to designated operations, the CAFO should
submit documentation as to how the conditions
were addressed and why the operation is no longer
a significant contributor of pollutants to waters of
the U.S. In those cases where there is a significant
reduction in the number of animals being confined,
the permitting authority should request records
that document the proper disposition of any
stored manure and wastewater on the basis of the
permitted capacity of the operation.

4.3.3. Manure Transfer Requirements for Large CAFOs
NPDES permits for Large CAFOs must include specific requirements concerning the transfer
of manure to other persons. The permit must require the operator to provide all recipients of
manure and wastewater generated by the CAFO with the most current manure nutrient analysis.
40 CFR § 122.42(e)(3). The nutrient analysis must be consistent with the CAFO ELG. 40 CFR § 412.
The ELG for Large CAFOs requires that manure be sampled for nitrogen and phosphorus at least
annually. In addition, the permit must require Large CAFOs to retain records of the date of the
transfer, the name and address of the recipient, and the approximate amount of manure, litter,
or process wastewater transferred (tons/gallons). Those records are to be maintained for 5 years
from the date the manure, litter, or process wastewater is transferred. As a result of the negative
environmental impact of the improper use and disposal of manure, NPDES permit writers should
use PBJ in determining whether to include these requirements in an NPDES permit issued to a
small or medium CAFO. For examples of a manure, litter, and wastewater transfer record form,
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit

4.3.3. Manure Transfer Requirements for Large CAFOs

4-48

NPDES Permit Writers’ Manual for CAFOs

see Appendix P, Sample Nutrient Management Plan Section 7 and Appendix D, Example Nutrient
Management Plan Recordkeeping Forms.

4.4. Standard Conditions of a CAFO NPDES Permit
Standard conditions must be included in all NPDES permits. Standard conditions specified
in 40 CFR parts 122.41 and 122.42 play an important supporting role to effluent limitations,
monitoring and reporting requirements, and special conditions because they delineate
various legal, administrative, and procedural requirements of the permit. Standard conditions
cover various topics, including definitions, testing procedures, records retention, notification
requirements, penalties for noncompliance, and other permittee responsibilities. The conditions
provided in 40 CFR part 122.41 apply to all types and categories of NPDES permits and must be
included in all permits (for applicability to state NPDES permits, see 40 CFR part 123.25). The
conditions provided in 40 CFR part 122.42 apply to only certain categories of NPDES facilities.
Any permit issued to a facility in one of the categories listed in 40 CFR part 122.42 must contain
the additional conditions, as applicable.
The use of standard conditions helps ensure uniformity and consistency of NPDES permits issued
by authorized states or the EPA Regional offices. Permit writers need to be aware of the contents
of the standard conditions because it might be necessary to explain portions of the conditions to a
discharger. The permit writer should keep abreast of any changes in EPA’s standard conditions set
out in 40 CFR parts 122.41 and 122.42. According to 40 CFR part 122.41, standard conditions may
be incorporated into a permit either expressly (verbatim from the regulations) or by reference
to the regulations. It generally is preferable for permit writers to attach the standard conditions
expressly because permittees might not have easy access to the regulations. Some states have
developed an attachment for NPDES permits that includes the federal standard conditions.

4.4.1. Types of Standard Conditions
A brief summary of the 40 CFR part 122.41 standard conditions that must be included in all types
of NPDES permits follows:
▶ Duty to Comply 40 CFR part 122.41(a): The permittee must comply with all conditions
of the permit. Noncompliance is a violation of the CWA and is grounds for enforcement
action, changes to or termination of the permit, or denial of a permit renewal
application.
▶ Duty to Reapply 40 CFR part 122.41(b): A permittee wishing to continue permitted
activities after the permit expiration date must reapply for and obtain a new permit.
▶ Need to Halt or Reduce Activity not a Defense 40 CFR part 122.41(c): The permittee
may not use as a defense in an enforcement action the reasoning that halting or
reducing the permitted activity is the only way to maintain compliance.

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit
4.4.1. Types of Standard Conditions

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NPDES Permit Writers’ Manual for CAFOs

▶ Duty to Mitigate 40 CFR part 122.41(d): The permittee is required to take all reasonable
steps to prevent any discharge or sludge use or disposal in violation of the permit that
has a reasonable likelihood of adversely affecting human health or the environment.
▶ Proper Operation and Maintenance 40 CFR part 122.41(e): The permittee must
properly operate and maintain all equipment and treatment systems used for
compliance with the terms of the permit. The permittee must provide appropriate
laboratory controls and quality assurance procedures. Operation of backup systems is
required only when needed to ensure compliance.
▶ Permit Actions 40 CFR part 122.41(f): The permit may be modified, revoked and
reissued, or termin­ated for cause. A request by the permittee for a permit modification,
revocation or reissuance, termination, or a notification of planned changes or
anticipated non­compliance does not suspend the permittee’s obligation to comply with
all permit conditions.
▶ Property Rights 40 CFR part 122.41(g): The permit does not convey any property rights
of any sort, or any exclusive privilege.
▶ Duty to Provide Information 40 CFR part 122.41(h): The permittee must furnish,
within a reasonable time, any information needed to determine compliance with
the permit or to determine whether there is cause to modify, revoke and reissue, or
terminate the permit. The permittee also must furnish, on request, copies of records
that must be kept as required by the permit.
▶ Inspection and Entry 40 CFR part 122.41(i): The permittee must, on presentation
of valid credentials by the Director or his or her representative, allow entry into the
premises where the regulated activity or records are present. The Director must
have access to and be able to make copies of any required records; inspect facilities,
practices, operations, and equipment; and sample or monitor at reasonable times.
▶ Monitoring and Records 40 CFR part 122.41(j): Samples must be representative of the
monitored activity. The permittee must retain records for 3 years (5 years for sewage
sludge activities) subject to extension by the Director. Monitoring records must identify
the sampling dates and personnel, the sample location and time, and the analytical
techniques used and corresponding results. Wastewater and sludge measurements
must be conducted in accordance with Parts 136 or 503 or other specified procedures.
Falsification of results is a violation under the CWA.
▶ Signatory Requirement 40 CFR part 122.41(k): The permittee must sign and certify
applications, reports, or information submitted to the Director in accordance with the
requirements in 40 CFR § 122.22. Knowingly making false statements, representations,
or certifications is punishable by fines or imprisonment.
▶ Planned Changes 40 CFR part 122.41(l)(1): Notice must be given to the Director as
soon as possible of planned physical alterations or additions to the facility (or both)

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit
4.4.1. Types of Standard Conditions

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NPDES Permit Writers’ Manual for CAFOs

that could meet the criteria for determining whether the facility is a new source
under 40 CFR part 122.29(b); result in changes in the nature or quantity of pollutants
discharged; or significantly change sludge use or disposal practices.
▶ Anticipated Noncompliance 40 CFR part 122.41(l)(2): The permittee must give
advance notice of any planned changes that could result in noncompliance.
▶ Permit Transfers 40 CFR part 122.41(l)(3): The permit is not transferable except after
written notice to the Director. The Director may require modification or revocation and
reissuance, as necessary.
▶ Monitoring Reports 40 CFR part 122.41(l)(4): [This standard condition is not applicable
to CAFOs because CAFOs are not required to maintain and submit discharge
monitoring reports (DMRs).]
▶ Twenty-Four Hour Reporting 40 CFR part 22.41(l)(6): The permittee must orally report
any noncompliance that might endanger human health or the environment within 24
hours after becoming aware of the circumstances. Within 5 days of becoming aware
of the circumstances, the permittee must provide a written submission including
a description of the noncompliance and its cause; the period of noncompliance,
including exact dates and times; the anticipated time the noncompliance is expected
to continue (if not already corrected); and steps taken to reduce, eliminate, or prevent
reoccurrence unless the Director waives the requirement. In addition, 24-hour
reporting is required for an unanticipated bypass exceeding effluent limits; an upset
exceeding effluent limits; and a violation of a maximum daily effluent limitation for
pollutants listed in the permit for 24-hour reporting.
▶ Other Noncompliance 40 CFR part 122.41(l)(7): The permittee must report all
instances of noncompliance not reported under other specific reporting requirements
at the time monitoring reports are submitted.
▶ Other Information 40 CFR part 122.41(l)(8): If the permittee becomes aware that
it failed to submit any relevant facts in its application, or submitted incorrect
information in its application or other reports, it must promptly submit such facts or
information.
▶ Bypass 40 CFR part 122.41(m): The intentional diversion of wastestreams from any
portion of a treatment facility. Bypass is prohibited unless the bypass does not cause
the effluent to exceed limits and is for essential maintenance to ensure efficient
operation (no notice or 24-hour reporting is required in such a case). All other bypasses
are prohibited, and the Director of the NPDES program may take enforcement action
against a permittee for a bypass, unless the bypass was unavoidable to prevent loss of
life, personal injury, or severe property damage; there was no feasible alternative; and
the proper notification was submitted.
▶ Upset 40 CFR part 122.41(n): An upset (i.e., an exceptional incident in which there is
unintentional and temporary noncompliance with technology-based effluent limits
4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit
4.4.1. Types of Standard Conditions

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NPDES Permit Writers’ Manual for CAFOs

because of factors beyond the permittee’s control) can be used as an affirmative
defense in actions brought against the permittee for noncompliance. An upset does not
include noncompliance to the extent caused by operational error, improperly designed
or inadequate treatment facilities, lack of preventative maintenance, or careless or
improper operation. The permittee (who has the burden of proof to demonstrate that
an upset has occurred) must have operational logs or other evidence that shows
• When the upset occurred and its causes.
• The facility was being operated properly.
• Proper notification was made.
• Remedial measures were taken.

Reference
USEPA (U.S. Environmental Protection Agency). 1992. NPDES Storm Water Program Question
and Answer Document Volume 1. EPA 833-F-93-002. U.S. Environmental Protection Agency,
Washington, DC.

Endnotes
Except that subpart B applies to operations with 5,000 or more ducks, and does not distinguish between dry and
liquid manure handling systems.

1

Appendix F, Voluntary Alternative Performance Standards for CAFOs presents an overview of the baseline
requirements and the voluntary performance standards program, which includes a description of who can
participate in the program and how participation in the program will affect existing NPDES CAFO permits, as well
as a step-by-step description of the requirements associated with participation in the program.

2

Including the additional measures and record-keeping requirements specified in 40 CFR parts 412.37(a) and (b).

3

The discussion in this section does not address discharges that qualify as exempt agricultural stormwater. For a
discussion of the agricultural stormwater exemption, see Section 4.1.8.

4

See 40 CFR part 122.23(e), 68 FR 7176 at 7196 (February 12, 2003) and Revised NPDES Regulation and ELGs for
CAFOs in Response to the Waterkeeper Decision, 73 FR 70418, 70434 (November 20, 2008).

5

73 FR 70434.

6

4. Elements of an NPDES Permit for a CAFO
4.1. NPDES Effluent Limitations and
Standards

4.2. Monitoring, Record-Keeping, and
Reporting Requirements of NPDES
Permits for CAFOs

4.3. Special Conditions for All NPDES
Permits for CAFOs

4.4. Standard Conditions of a CAFO NPDES
Permit
4.4.1. Types of Standard Conditions

5-1

NPDES Permit Writers’ Manual for CAFOs

Chapter

5

5. Nutrient Management Planning
An NMP helps a CAFO owner or operator to ensure that crop needs are met while minimizing
impacts on water quality. Most commonly, NMPs are used to develop appropriate rates for
the application of manure and fertilizer. However, they can also include an array of other
management and conservation practices to optimize the productivity of the operation while
conserving nutrients and protecting the environment. Those include practices such as
appropriate manure and fertilizer storage and handling methods, managing the diet of the
animals, or irrigation practices. The CAFO regulations specify nine minimum requirements
that must be included in an NMP, to the extent that they are applicable, for any CAFO seeking
permit coverage. 40 CFR § 122.42(e)(1). The permit writer must incorporate conditions that
address those NMP requirements into the permit as enforceable permit terms. The permit terms
must include the information, protocols, BMPs and other conditions identified in a CAFO’s
NMP that are necessary to meet the nine minimum requirements. 40 CFR § 122.42(e)(5). For
permitted Large CAFOs, the permit terms must also include the requirements of the ELG.
40 CFR §§ 122.42(e)(5), 412.4.
This chapter discusses each of the required nine minimum requirements that CAFOs
must address in an NMP and how to develop enforceable permit terms for each minimum
requirements (with the exception of land application protocols, which is addressed in
Chapter 6). In addition, this chapter discusses the ELG requirements applicable to permitted
Large CAFOs. Where applicable, the chapter also includes technical information to provide
the permit writer with background information and understanding that will help support
development of site-specific terms for certain minimum NMP requirements.

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NPDES Permit Writers’ Manual for CAFOs

5.1. EPA’s Nine Minimum Requirements for Nutrient
Management
Any permit issued to a CAFO of any size must include a requirement to implement an NMP that
contains, at a minimum, BMPs that meet the requirements specified in 40 CFR part 122.42(e)(1).
Those consist of the following:
1. Ensuring adequate storage of manure, including procedures to ensure proper O&M of
the storage facility.
2. Managing mortalities to ensure that they are not disposed of in a liquid manure,
stormwater, or process wastewater storage or treatment system that is not specifically
designed to treat animal mortalities.
3. Ensuring that clean water is diverted, as appropriate, from the production area.
4. Preventing direct contact of confined animals with waters of the U.S.
5. Ensuring that chemicals and other contaminants handled on-site are not disposed of
in any manure, litter, process wastewater, or stormwater storage or treatment system
unless specifically designed to treat such chemicals and other contaminants.
6. Identifying appropriate site-specific conservation practices to be implemented,
including as appropriate buffers or equivalent practices, that control runoff of pollutants
to waters of the U.S.
7. Identifying protocols for appropriate testing of manure, litter, process wastewater,
and soil.
8. Establishing protocols to land apply
manure, litter, or process wastewater in
accordance with site-specific nutrient
management practices that ensure
appropriate agricultural utilization of
the nutrients in the manure, litter or
process wastewater.
9. Identifying specific records that
will be maintained to document the
implementation and management of the
minimum elements described above.

NRCS and landowner on dairy farm discuss NMP
requirements. (Photo courtesy of USDA/NRCS)

The ways in which permitted CAFOs must
address those requirements in their NMPs
differ and are discussed in more detail in the
sections below.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

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NPDES Permit Writers’ Manual for CAFOs

5.1.1. Permitted Large CAFOs
Permitted Large CAFOs must implement
NMPs as a condition of their permits.
40 CFR § 122.42(e)(1). At a minimum, the
NMPs must address the requirements
of 40 CFR part 122.42(e)(1). Additionally,
permitted Large CAFOs are subject to the ELG
defined at 40 CFR part 412. The ELG require
specific standards for implementing land
application rates, manure and soil sampling,
and conservation practices, among other
requirements. For an introduction of the ELG
requirements, see Chapter 4.1.1. The ELG
requirements relevant to land application are
discussed in detail in the appropriate sections
below.

A permitted Large CAFO in California that must implement
an NMP as a condition of their permit. (Photo courtesy of
USDA/NRCS)

5.1.2. Permitted Small and Medium CAFOs
Like all permitted CAFOs, Small and Medium CAFOs must develop and implement NMPs that
address the requirements of 40 CFR part 122.42(e)(1). However, Small and Medium CAFOs are
not subject to the ELG of 40 CFR part 412. Effluent limitations that build on part 122.42(e)(1) for
Medium and Small CAFOs are based on the BPJ of the permit writer. Permit writers might find
that it is appropriate to include BPJ effluent limitations that are the same as or similar to the
effluent limitations established in the ELG for Large CAFOs. (See Chapter 4.1.4.)

5.1.3. Unpermitted Large CAFOs
Unpermitted Large CAFOs are not required to implement an NMP. However, for precipitationrelated discharges from the land application area to qualify as agricultural stormwater exempt
from permit requirements, unpermitted CAFOs must develop and implement the nutrient
management practices specified by 40 CFR part 122.42(e)(vi)–(ix) to ensure appropriate
agricultural utilization of the nutrients in the manure being land applied. That means that the
CAFO’s nutrient management planning must account for appropriate site-specific conservation
practices, protocols for appropriate manure and soil testing, appropriate protocols for land
application, and maintenance of records to document the implementation of those BMPs. EPA
recommends that unpermitted Large CAFOs with precipitation-related land application area
discharges develop and implement NMPs similar to permitted operations. By doing so, the
operator can ensure that proper practices are implemented and documented to demonstrate
that any discharge from the land application area is agricultural stormwater. For a more
detailed discussion on the requirements for meeting the agricultural stormwater exemption, see
Chapter 4.1.8.
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.1.3. Unpermitted Large CAFOs
5.7. Chemical Disposal

5.8. Conservation Practices

5-4

NPDES Permit Writers’ Manual for CAFOs

5.2. Developing Permit Terms
Section 4.1.7 includes a discussion of options for capturing the nine minimum requirements
as broadly applicable permit terms, site-specific terms, or some combination of both in which
a broadly applicable permit term can be supplemented with a site-specific term. To the extent
that the NMP provides site-specific information about practices that are necessary to comply
with one of the minimum requirements, that information can be included as all or part of each
permit term. Ultimately though, it is up to the permitting authority to determine the extent to
which site-specific information from the NMP is necessary or sufficient to adequately capture
each of the nine minimum requirements as permit terms. The exception is the requirement
to establish protocols for land application, which can be captured as a site-specific term only.
40 CFR § 122.42(e)(5). Note that the public can comment on the sufficiency or applicability of the
terms of the NMP.
There could be cases where no site-specific information is
provided in the NMP for several of the NMP requirements.
For example, diversion of clean water from the production
area might not be applicable to some CAFO’s operation.
Another example is where the permit simply prohibits
direct contact of animals with waters of the U.S. Where
site-specific information on a requirement is not necessary
to include in an NMP, a broadly applicable term, rather
than a site-specific term, will be sufficient. In other cases, a
broadly applicable term may be used in the general permit
and more specific information will be needed in the NMP
submitted with the NOI to explain how the facility will
meet the general permit conditions. The issue is discussed
in greater detail under each of the NMP requirements
where it is appropriate.

NRCS staff discuss conservation planning with a
landowner next to a stream livestock exclusion
fence in Van Buren County, Michigan.
(Photo courtesy of USDA/NRCS)

NMP requirements may be addressed through the use of
one or more of USDA’s conservation practice standards
where the standards meet applicable state requirements,
as long as they are identified in the operation’s site-specific
NMP and appropriate O&M activities are identified. A
USDA conservation practice standard may be captured as a
site-specific term, or when appropriate, it may be identified
as a broadly applicable term. NRCS’s standards are
identified in USDA’s Comprehensive Nutrient Management
Plans and National Instruction (USDA-NRCS 2009). The
practice standards are also included in each state NRCS
Field Office Technical Guides. The sections below identify

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-5

NPDES Permit Writers’ Manual for CAFOs

NRCS Conservation Practice Standards associated with the technical basis for each of the
minimum NMP requirements. Appendix K, NRCS Conservation Practice Standards, provides a
description of each of the practice standards included in this chapter.
The remainder of this chapter discusses the components of seven of the nine minimum
requirements. The requirements for maintaining records and protocols for land application are
discussed in detail, respectively, in Chapters 4.2 and 6.5. This chapter includes basic technical
guidance as to how each requirement can be implemented. The guidance is further illustrated
with examples of site-specific information that is likely to be found in an NMP. Permit writers
should consider such examples to be a starting point for identifying the information in an NMP
that constitute the permit terms necessary to capture the nine minimum requirements. For cases
where the basis for the applicable permit term is a source other than a CAFO’s NMP, this chapter
also provides sample permit language that could be used for writing a broadly applicable term.

5.3. Adequate Manure, Litter, and Wastewater Storage,
Including Procedures to Ensure Proper Operation
and Maintenance of the Storage Facility
40 CFR Part 122.42(e)(i)
Permitted CAFOs must have an NMP that ensures adequate storage of manure, litter, and process
wastewater. The term adequate storage means that, at a minimum, the NMP must demonstrate
that the CAFO has sufficient storage capacity to ensure compliance with the effluent limitations
of the permit. For many permitted CAFOs, that requirement means that the CAFO must have, at a
minimum, sufficient storage capacity to ensure that the production area is designed constructed,
operated, and maintained to contain all manure, litter, and process wastewater including the
runoff and the direct precipitation from a 25-year, 24-hour rainfall event. 40 CFR §§ 412.13, 412.15,
412.26, and 412.31(a). For a detailed discussion of the applicable requirements for each animal
subpart, see Chapter 4.1.2. The terms of the permit must address all the conditions necessary to
ensure that the CAFO meets the requirements for adequate storage.
All manure, litter, and process wastewater storage structures must be properly designed,
constructed, operated, and maintained, regardless of where they are in relation to the animal
confinement area. That would include, for example, manure storage sites, such as litter stockpiles,
that are near fields where the manure or litter is to be spread. In addition, a well-designed
and constructed manure storage facility must be operated and maintained to prevent the
development of conditions that could lead to a discharge. Management decisions relative to
startup and loading (especially for anaerobic lagoons), manure removal, monitoring of structural
integrity, and maintenance of appearance and aesthetics play critical roles in well-managed
storage facilities.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-6

NPDES Permit Writers’ Manual for CAFOs

5.3.1. Permit Terms for Adequate Storage of Manure, Litter,
and Wastewater
The practices and information required by the permit, including any applicable standard by
which wastewater and manure storage structures are to be designed, constructed, operated,
and maintained need to be identified by the permitting authority and should be included in the
permit term as either a site-specific term or a broadly applicable permit term. The principle sitespecific terms for adequate storage capacity typically include the following:
▶ The structures used to provide adequate manure storage and the storage capacity of
each structure.
▶ The facility’s critical storage period—the time that would result in maximum
production of manure and wastewater anticipated between emptying events—and
emptying schedules (see the Agitation text box on page 5-15).
▶ The total design volume—for example, for facilities subject to the 25-year, 24-hour
storm standard, the volume generated during the critical storage period plus the
25-year, 24-hour storm event volume plus the storage structure freeboard and other
required design components (see more detailed explanation in Section 5.3.2).
▶ Off-site transport practices, including frequency and amount of off-site transfers, to the
extent that the practices are critical to ensuring adequate storage.
For adequate storage, O&M requirements should also be included as part of the site-specific
permit term 40 CFR parts 122.42(e)(1)(i) and (e)(5). Section 5.3.2 discusses O&M procedures for
storage structures in greater detail. Typical O&M activities that might be included as site-specific
terms include the following:
▶ Frequency of inspections of storage structures to confirm they are maintaining
adequate storage capacity. Regulations at 40 CFR part 412 require weekly inspections
for Large permitted subpart C and D CAFOs.
▶ Removal of solids from storage structures as needed to maintain the design storage
capacity.
▶ Removing manure or wastewater or both in accordance with the NMP and the
structure’s design storage capacity (see the discussions of storage structure design and
critical storage period above).
▶ Maintaining storage capacity for the design storm event (25-year, 24-hour storm
event for most permitted Large CAFOs and the storm event dictated by site-specific
management practices for open containment systems to meet the no discharge
standard for new permitted Large swine, poultry, and veal calf CAFOs). The
regulations at 40 CFR parts 412.37 and 412.47 require that all open surface liquid

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.3.1. Permit Terms
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5-7

NPDES Permit Writers’ Manual for CAFOs

impoundments must have a depth marker that clearly indicates the minimum capacity
necessary to contain the runoff and direct precipitation of the 25-year, 24-hour rainfall
event.
▶ Maintenance of any controls that are used to prevent plants and burrowing animals
from eroding storage structure berms, embankments, liners, and sidewalls.
▶ Maintenance of vegetation, rock, or other materials used to prevent erosion and
stabilize berms and embankments.
▶ Maintenance of any structures necessary (i.e., fencing) that is used to prevent animal
access to the storage area.
▶ Inspections to ensure that all inlets and outlets to the storage structure are not blocked
by debris or ice.
▶ Inspections of the perimeter of any storage structure to ensure any runoff or process
wastewater is contained and repairing any deficiencies identified.
While some elements of adequate storage can be broadly applicable to all facilities, EPA
believes that some elements need to be site-specific to fully meet the requirements of
40 CFR part 122.42(e)(1)(i).

Proper O&M standard permit condition
Proper O&M is a standard condition required to be included in all NPDES permits.
40 CFR § 122.41(e). Proper O&M of storage structures includes activities such as
periodic solids removal to maintain storage capacity, maintenance of berms and
sidewalls, prompt repair of any deficiencies, and, for liquid manure storage structures,
appropriate dewatering activities. The standard condition does not provide enough
specificity to detail the extent of O&M that should be conducted at a CAFO.

As discussed, in some instances NRCS practices standards can be included (as either a broadly
applicable term, a site-specific term or a site-specific term that is used to supplement a broadly
applicable term) as part of the permit terms and conditions. Table 5-1 identifies the technical
basis for the NMP minimum practice to ensure adequate storage and some related NRCS
conservation practice standards that might be included in NMPs to address the minimum
requirement. Where references are made to NRCS standards, permit writers should ensure that
necessary O&M actions are also included as permit terms. Appendix K, NRCS Conservation
Practice Standards, includes a description of those conservation practice standards.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.3.1. Permit Terms
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5-8

NPDES Permit Writers’ Manual for CAFOs

Table 5-1. EPA minimum practice/NRCS conservation practice comparison
NPDES NMP
minimum
practice
Ensure
adequate
storage

Associated NRCS conservation
practice standards

Technical basis
Maintaining sufficient storage capacity
is critical for a CAFO to be able to
properly store manure, wastewater,
and stormwater for those periods when
land application is not appropriate. A
CAFO’s ability to meet the applicable
nutrient management technical standard
depends on proper storage practices.
Insufficient storage capacity increases the
risk of runoff from manure piles and spills
from lagoons and other containment
structures. It also increases the possibility
that an operation will have to land apply
during periods of increased risk to surface
water (e.g., during rainfall events).

Waste Storage Facility - NRCS Practice
Standard Code 313
Composting Facility - NRCS Practice
Standard Code 317
Waste Treatment Lagoon NRCS Practice Standard Code 359
Anaerobic Digester - NRCS Practice
Standard Code 366
Roofs and Covers - NRCS Practice
Standard Code 367
Solid/Liquid Waste Separation Facility NRCS Practice Standard Code 632

5.3.2. Technical Information on Storage Structure Design,
Construction, Operation and Maintenance
Design and Construction of Storage Structures
Liquid Manure Storage Structures
Liquid manure storage structures have unique requirements that must be addressed to ensure
adequate storage of liquid waste. Such structures must have adequate capacity to contain the
volume accumulated as a result of contributions from all sources.
The total design volume for a liquid manure storage structure from a facility subject to the
25‑year, 24-hour size storm standard required in Part 412 must include an allowance for each of
the following:
▶ The volume of manure, process wastewater, and other wastes accumulated during the
storage period (see the discussion of critical storage period below).
▶ The volume of normal precipitation minus evaporation on the storage structure surface
during the entire storage period.
▶ The volume of runoff from the facility’s drainage area from normal rainfall events
during the storage period.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-9

NPDES Permit Writers’ Manual for CAFOs

▶ The volume of precipitation from the 25-year,
24‑hour rainfall event on the storage structure
surface.
▶ The volume of runoff from the facility’s drainage area
from the 25-year, 24-hour rainfall event.
▶ The volume of any leachate from bunk silos or other
silage storage areas.
▶ In the case of anaerobic waste treatment lagoons, the
minimum treatment volume.
▶ The minimum volume to maintain the integrity of
the lagoon bottom.

CAFO waste lagoon—a liquid manure storage
structure. (Photo courtesy of USDA/MO NRCS)

▶ The volume of solids remaining in a storage structure after liquids are removed.
▶ Any necessary freeboard required to maintain structural integrity, although that is not
considered to be a component of the structure’s storage volume.
The volume of normal precipitation for the storage period should reflect the maximum amount of
rainfall to be expected between emptying events. For example, if a storage structure is dewatered
once every 6 months, the volume of normal precipitation should reflect the precipitation that is
expected during the wetter of the two 6-month storage periods.
When a series of rainfall events precludes dewatering, the remaining capacity of the storage
structure is reduced. When dewatering is not possible, a rainfall event of any size, both smaller
or larger than the 25-year, 24-hour storm event, could result in an overflow that complies with
effluent limitations based on 40 CFR part 412. CAFOs that do not actively maintain the capacity
of the storage structure, such as CAFOs that start dewatering only when the storage structure
is completely full, are not entitled to such discharge authorization (see the discussion of proper
O&M below). It is unlikely that any given series of storms would result in an overflow from a
properly developed liquid storage structure, unless the series of storms occurs so close to the
end of the design storage period that the storage structure is already filled close to capacity at the
beginning of the chronic rainfall event.
The volume needed for solids accumulation in a liquid manure storage structure varies with
the presence and efficiency of solids separation equipment or processes and the extent to which
the storage structure provides treatment. The total volume needed for solids accumulation also
depends on the length of time between solids removal. Operational practices can also affect the
volume needed for solids accumulation. For example, facilities that completely agitate a manure
pit before pumping are likely to need less long-term solids storage volume than facilities that only
pump liquid from the top of the storage structure, although it is generally advisable to agitate.
(See the Agitation text box on page 5-15.) Facilities that do not intend to remove solids for many
years at a time will need to provide solids storage volume for that entire period.
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-10

NPDES Permit Writers’ Manual for CAFOs

Terminology for Storage Structures
These terms are not defined by EPA in the NPDES regulations, but the following definitions are
useful for understanding and properly implementing the regulations.

Freeboard
EPA encourages the use of NRCS and American Society of Agricultural and Biological Engineers
(ASABE) standards that use the term freeboard to describe a safety feature for an open liquid
storage system, to protect the integrity of the berm. Freeboard should not be treated as volume
for additional storage capacity but as a structural feature necessary to the proper design of a
liquid storage system.

Critical Storage Period
The minimum design volume for liquid manure storage structures is based on the expected
length of time between emptying events that result in maximum production of process
wastewater, including runoff from the production area. That period is the critical storage
period.
The critical storage period might not necessarily be the maximum period between emptying
events. For example, in an area that receives most of its annual rainfall over 3 months, more
process wastewater might be generated over a 4-month storage period that includes the rainy
season than over an 8-month dry period.

Chronic Rainfall
Chronic rainfall is considered to be a series of wet-weather conditions that could preclude
dewatering of liquid retention structures. A permitted CAFO’s storage structure needs to have
capacity for the critical storage period, thus accommodating all wastes, precipitation, and
runoff that might accumulate during that period. Therefore, properly designed systems need
to account for periods of heavy rainfall that might occur during periods when a state’s technical
standard prohibits land application or when the CAFO is otherwise unable to land apply.
When, however, excessive rainfall causes discharges from storage structures that are properly
designed, constructed, operated, and maintained to meet the requirements of a CAFO’s
permit, such discharges may be allowable discharges under the permit, or may qualify under
the upset/bypass provisions of the regulations.

Additional standards and criteria for storage structures might also be required to meet
management goals or other regulatory and state requirements. For example, a state could require
CAFOs to follow recommendations from the NRCS National Engineering Handbook Part 651
Agricultural Waste Management Field Handbook (USDA-NRCS 1999) or NRCS conservation
practice standards 313 Waste Storage Facility and 359 Waste Treatment Lagoon (USDA-NRCS
2003). Those practice standards include information on the foundation of the storage pond or
lagoon, maximum operating levels, structural loadings for fabricated structures, slab designs,
and considerations for minimizing the potential for and effects of sudden breach of embankment
or accidental release. Large dairy, beef, poultry, swine, and veal calf CAFOs must identify the
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-11

NPDES Permit Writers’ Manual for CAFOs

site‑specific design basis in their records and maintain a copy of the records on-site (as required
by 40 CFR part 412.37(b)(5), discussed in Section 4.2.2). All CAFOs should maintain similar
records to ensure adequate storage and prevent discharges.

Treatment Lagoon Design
One reference for design of an anaerobic lagoon is the ANSI/ASAE standard EP403.3 entitled
Design of Anaerobic Lagoons for Animal Waste Management. ASAE’s standard on the design of
anaerobic lagoons states that the lagoon depth should provide for a 6.6-foot minimum depth
when the lagoon is filled to its treatment volume elevation, which should be at least 1 foot above
the highest groundwater table elevation. ASAE also recommends making the lagoon as deep
as practical to reduce surface area and convection heat loss, enhance internal mixing, reduce
odor emissions, promote anaerobic conditions, minimize shoreline weed growth problems, and
reduce mosquito production. This standard also provides equations for calculating the total
lagoon volume and a listing of recommended maximum loading rates for anaerobic lagoons for
animal waste in mass of volatile solids per day per unit of lagoon volume. The treatment volume
is sized on the basis of waste load (volatile solids or VS) added per unit of volume and climatic
region. Maximum lagoon loading rates are usually based on average monthly temperature and
corresponding biological activity. If odors are of concern, consideration is also given to reducing
the VS loading.
The NRCS Standard Practice 359 Waste Treatment Lagoon provides information on minimum top
widths, operating levels, embankment elevations, and considerations for minimizing the potential
of lagoon liner seepage.
Other frequently used references are NRCS’ Agricultural Waste Management Field Handbook,
Part 651, National Engineering Handbook, ASAE Engineering Practice standard ASAE EP393.3
Manure Storages, and Midwest Plan Service publication MWPS-18.

Figure 5-1. Cross section of properly designed lagoon

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-12

NPDES Permit Writers’ Manual for CAFOs

Solid Manure Storage Structures
Solid manure storage structures include storage areas such as the lower level of high-rise poultry
houses, sheds for poultry litter, pits, stockpiles, mounds in dry lots, compost piles, and pads.
The storage capacity of a solid manure storage structure should consider the frequency at which
manure is moved from confinement areas to the storage structure and frequency at which
manure will be removed from the storage structure for land application or off-site transfer.
Because all water that contacts raw materials, products, or by-products, including manure and
litter, is considered to be process wastewater, CAFOs must manage runoff from any solid manure
storage areas that are exposed to precipitation. CAFOs should consider storing stockpiles of solid
manure and litter under a roof to exclude precipitation whenever possible to reduce or eliminate
the need to collect all runoff from the
stockpile. Solid manure and litter stockpiles
that are not stored under a roof should be
covered to exclude precipitation whenever
possible. Where it is not possible to cover
stockpiles that are stored for more than 15
days, the stockpile constitutes a liquid manure
handling system. For chickens and duck
sectors, a lower CAFO threshold would apply
(see Section 2.2.4).
Permit authorities may also require CAFOs to
manage seepage to groundwater from solid
manure storage areas. The floor of a solid
manure storage area should be constructed
of compacted clay, concrete, or other material
designed to minimize the leaching of wastes
beneath the storage area. The floor should
be sloped toward a collection area or sump
so that runoff or leachate can be collected
and transferred to a liquid manure storage
structure or treatment system.

Solid manure structures include composter piles.
(Photo courtesy of USDA/MO NRCS)

O&M of Storage Structures
All manure storage structures must be
operated and maintained to prevent the
discharge of pollutants into waters of the
U.S. Frequent overflows are a potential
indicator that a CAFO is not meeting its permit
obligations to ensure adequate storage and to
properly operate and maintain the facility.

Inspecting compost from turkey manure and woodchips
storage structure. (Photo courtesy of USDA/NRCS)
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-13

NPDES Permit Writers’ Manual for CAFOs

In general, the records maintained by the operator help determine
whether proper O&M has been performed. For Large subpart C
and D CAFOs, the ELG specifies some of the records that must
be maintained. NPDES permits for all CAFOs should specifically
identify any records necessary to document implementation of the
O&M practices required by the permit.
This section highlights activities at CAFOs that are related to O&M
of manure storage and handling structures and the types of records
that can be maintained to document implementation of such
practices.

Storage facility maintenance is
essential. (Source: EPA Region 10)

Manure Removal
The most important consideration in operating and maintaining a liquid manure storage
structure is to ensure that the structure does not overflow and that the manure and wastewater
is removed when it is appropriate to do so. Many discharge problems have occurred because
producers were unable to manage the activities necessary to remove manure from storage in a
timely manner. The appropriate frequency of emptying events could be based on factors such as
the following:
▶ Storage structure size (i.e., if it contains more than the minimum required storage
capacity).
▶ Hydraulic limitations of a land application site.
▶ Typical precipitation for the area.
▶ Nutrient concentrations in the stored manure or wastewater.
▶ Allowable timing of land application such as winter applications as specified in an
NMP.
▶ The extent to which the liquid in the storage structure is used for irrigation water.
▶ The cropping system included in a CAFO’s NMP.
Storage capacity should be sufficient to allow the CAFO to land apply at the times specified by
the land application schedule in the NMP. Low manure storage capacity might require frequent
applications and, possibly, year-round cropping systems, while larger storage volumes could
allow less frequent applications or less intensive cropping. For existing facilities, the storage
volume should be known or calculated, and the NMP should plan for land application (or other
manure use or disposal) frequently enough to ensure that the storage capacity is not exceeded.
The storage capacity for new facilities should be calculated to accommodate the planned
cropping system.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-14

NPDES Permit Writers’ Manual for CAFOs

Manure Removal Methods1
Solid Manure
Solid manure is usually removed from storage using front-end loaders, scrapers, or other bulkhandling equipment. The size of the equipment influences the time required to load hauling
equipment. Hauling equipment includes a truck-mounted beater, flail or spinner-type spreader
boxes, and pull-type spreaders. The size or volume of the hauling equipment used influences the
number of trips required to empty manure storage facilities. The hauling distance determines the
time necessary to complete a trip.

Litter
Litter is usually removed from storage using the same type of equipment as used for solid
manure. Care should be taken to minimize the amount of litter that is spilled on the ground when
removing litter from a poultry house. Construction of concrete pads at the entrance to poultry
houses can provide for easy cleanup and reduce the potential for runoff and infiltration.

Slurry Manure
Slurry manure should be agitated before and during pumping of the manure from storage.
Agitation equipment should be selected to provide sufficient homogenization of the slurry in an
acceptable time. Agitation is usually begun several hours before hauling and continued during
the hauling operation. Heavy-duty chopper pumps are generally used to load slurry-hauling
equipment. Hauling equipment includes conventional tank wagons and some box-type spreaders
designed to haul slurry. The flow rate capability of the loading pump determines the time
required to load, and the size or volume of the hauling equipment determines the number of trips
that must be made. Hauling distance is an important factor in total trip time.
Umbilical or drag-hose systems are also used in spreading slurry manure. The method offers the
advantage of continuous flow, and the slurry manure is injected or incorporated into the soil
during spreading. Soil compaction is reduced because a fully loaded manure spreader is not
pulled across the field. Emptying time with this method depends primarily on the pumping rate
through the drag hose. The use of a flow meter is recommended with the systems to ensure that
the manure is applied at the proper rate.

Liquid Manure
Liquid storage systems can be agitated. If they are not agitated, considerable nutrient buildup
in the sludge will occur and will be a factor when the sludge is agitated and removed. Because
solids in a liquid storage system tend to settle, nutrient concentrations vary at the surface, in the
sludge, or when agitated. If liquid storages are not agitated, their capacity will be reduced over
time because of solids buildup. Reduced capacity might not be obvious in treatment lagoons
where pump-down does not progress beyond the top liquid layer. Liquid storage system effluent
is usually removed by pumping equipment that might be similar to irrigation equipment. Hand
carry, solid set, stationary big gun, traveling gun, and center pivot equipment have all been used
to land apply lagoon effluent. Drag-hose systems are sometimes used as well. The pumping flow
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-15

NPDES Permit Writers’ Manual for CAFOs

rate of the system is the primary determining factor in the time required to pump down a liquid
storage system.
Agitation during manure removal is critical to maintaining available storage in many
liquid manure systems other than lagoons. Some facilities have designed storage
structures equipped with pumps to allow wastewater application without additional
agitation. Failure to properly agitate can result in a continued buildup of settled solids
that are not removed. The result is less and less available storage over time. Agitation of
manure re-suspends settled solids and ensures that most of or all the manure will flow to
the inlet of the pump or removal device. Additionally, agitation homogenizes the manure
mixture and provides more consistent nutrient content as the manure is being removed.
Manure samples for nutrient analysis should be obtained after the liquid or slurry storage
is well agitated. Agitation of manure storage facilities releases gases that can increase odor
levels and present a health hazard in enclosed spaces. Consideration should be given to
weather and wind conditions, time of day, and day of the week to minimize the possibility
of odor conflicts while agitating.

Monitoring and Recordkeeping
The regulations require all permitted CAFOs to identify in the NMP the specific records that will
be necessary to document proper implementation and management of the minimum required
elements for an NMP, which are discussed in Section 5.11. That includes the records necessary
to document the proper O&M of manure storage structures. 40 CFR § 122.42(e)(1)(ix). Records of
monitoring activities are a good indication that a CAFO is implementing proper O&M practices.

Regular Visual Inspections
All CAFO operators should regularly inspect the manure
storage structures to identify and correct problems with
structural integrity and storage capacity before a discharge
occurs. The frequency of inspections can vary, but a regular
inspection schedule should be developed and followed for
each handling and storage system. Inspection frequency might
depend on factors such as the system size and complexity,
the types of mechanical devices used (e.g., recycle pumps,
float switches in reception pits), the flow rate of the recycle
system, the proximity to a sensitive water source, and the type
of storage facility. The ELG regulations require that permitted
Large CAFOs conduct weekly inspections of all manure, litter,
and process wastewater impoundments. 40 CFR § 412.37(a)(1).
In addition to periodic inspections, manure levels in a storage
structure must be monitored and recorded weekly. The data
can illustrate the effects of excessive rainfall and lot runoff
and help in planning pump-down or other land application

Visual Inspections
§ 412.37(a)(1) There must be routine
visual inspections of the CAFO
production area. At a minimum, the
following must be visually inspected:
(i) Weekly inspections of all storm water
diversion devices, runoff diversion
structures, and devices channeling
contaminated storm water to the
wastewater and manure storage and
containment structure; (ii) Daily
inspection of water lines, including
drinking water or cooling water
lines; (iii) Weekly inspections of the
manure, litter, and process wastewater
impoundments; the inspection will note
the level in liquid impoundments as
indicated by the depth marker.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-16

NPDES Permit Writers’ Manual for CAFOs

activities. Manure levels should be observed and recorded frequently enough to provide a feel
for the rate of accumulation, and pumping activities should be scheduled accordingly. For Large
CAFOs, the ELG requires, at a minimum, weekly recording of manure and wastewater levels
in all liquid impoundments. 40 CFR § 412.37(b)(2). The permit writer can specify more frequent
monitoring of lagoon levels, if appropriate. 40 CFR § 122.41(j).

Depth Markers
A depth marker is a tool that allows CAFOs to manage the liquid level in an impoundment to
ensure that the impoundment has adequate capacity to contain direct precipitation and runoff
from the design rainfall event. Without a depth marker, impoundments could fill to a level above
their capacity, leading to overflows. The CAFO ELG requires Large CAFOs to install a depth
marker in all open surface liquid impoundments but level indicators are useful management
tools for all types of liquid impoundments. 40 CFR § 412.37(a)(2).
It is also a good practice to indicate the maximum drawdown level on the depth marker in a
treatment lagoon to ensure that the lagoon has the volume needed for biological treatment
and capacity for all solids accumulating between solids removal events. Figure 5-2 provides an
illustration of an open surface liquid impoundment with a depth marker.
CAFOs may use remote sensors
to measure the liquid levels in an
impoundment. Sensors can be
programmed to trigger an alarm
when the liquid level changes rapidly
or when the liquid level reaches a
critical level. The sensor can transmit
to a wireless receiver to alert the CAFO
about an impending problem. One
advantage of a remote sensor is that it
can provide CAFOs with a real-time
warning that the impoundment is in
danger of overflowing. CAFOs may use
remote sensors to track liquid levels
to supplement the weekly required
inspections of all manure and process
wastewater structures. Even though
remote sensors are more expansive, the
price may be offset by the additional
assurance they can provide in preventing
accidental discharge and circumventing
catastrophic failures.

Figure 5-2. Schematic of Lagoon Depth Marker

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.3.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-17

NPDES Permit Writers’ Manual for CAFOs

Rain Gauge
A simple rain gauge that indicates or records rainfall can be a useful tool in maintaining
and managing a manure storage structure. Rainfall has a significant impact on open storage
structures and structures serving open lots, so knowledge of rainfall amounts can be very useful.
A rain gauge can help with documenting such events without resorting to off-site data from
stations that might not be descriptive of conditions at the storage facility. Recorded rainfall data
are also evidence of good stewardship. While a rain gauge is not a regulatory requirement for
CAFOs, it can be a useful tool for the operator to provide documentation as to the intensity of a
storm event that resulted in a discharge.

Pumping Activities
“Experience has shown that unplanned discharges and spills sometimes occur with pumping
activities. Sources of such unplanned discharges include burst or ruptured piping, leaking joints,
operation of loading pumps past the full point of hauling equipment, and other factors. Thus,
pumping activities should be closely monitored, especially in the startup phase, to ensure that no
spills or discharges occur. Continuous pumping systems such as drag-hose or irrigation systems
can be equipped with automatic shutoff devices (which usually sense pressure) to minimize the
risk of discharge if pipe failure occurs.” (Harrison and Smith 2004b)

Liners
No NPDES or ELG regulatory requirements specifically concern the use of liners at CAFOs.
However, the permitting authority has the discretion to include additional special conditions in
NPDES permits for CAFOs beyond those required by the NPDES CAFO regulations where it has
determined that they are necessary to achieve effluent limitations and standards or carry out the
intent and purpose of the Clean Water Act (CWA). Such additional requirements might address,
for example, the use of liners in areas where there is the potential to discharge to groundwater
that has a direct hydrologic connection to waters of the U.S. Also, some states have permeability
or liner requirements that are based on state authorities other than the CWA.
“Liners in earthen manure storage impoundments are designed and constructed to provide an
additional barrier between the potential contaminants in the impoundment and groundwater.
Thus, liner integrity is extremely important in maintaining an environmentally sound manure
storage facility. Liners are constructed of compacted clay, geotextiles, or a combination of both.”
(Harrison and Smith 2004b)

5.4. Mortality Management 40 CFR 122.42(e)(ii)
Every permitted CAFO’s NMP must contain BMPs and protocols to ensure that mortalities are not
disposed of in a liquid manure, stormwater, or process wastewater storage or treatment system that
is not specifically designed to treat animal mortalities. In addition, Large CAFOs (except horse,
sheep, and duck CAFOs) must ensure that mortalities are handled in such a way as to prevent the
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-18

NPDES Permit Writers’ Manual for CAFOs

discharge of pollutants to waters of the U.S. 40 CFR 412.37(a)(4). Although that ELG requirement
does not apply to all permitted CAFOs, all CAFOs must ensure proper mortality handling.

5.4.1. Permit Terms for Mortality Management
The permit should require that the plan address both typical and catastrophic mortality. At a
minimum, the plan should identify the disposal method (which should account for the expected
mortality rate at the operation as discussed below), the location if applicable (which can include
sites for burial or sites of temporary storage until mortalities are removed off-site), and the actions
that are to be taken if a catastrophic mortality situation occurs. Site-specific terms could be the
specific structures or practices identified in the NMP and associated O&M practices including the
following:
▶ Schedules for collecting, storing, and disposing of carcasses.
▶ Description of on-site storage before disposal.
▶ Description of the final disposal method.
▶ Additional management practices to protect waters of the U.S. for on-site disposal
including composting or burial.
▶ Contingency plans for things such as mass mortality or loss of contract transporter for
rendering.
To the extent that broadly applicable permit terms meet the requirements above for ensuring
proper mortality management (including any necessary O&M), additional requirements might

Proper mortality management should preclude improper disposal of
animal carcasses as shown above. (Photo courtesy of USDA/MO NRCS)

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.11. Recordkeeping

5.12. Developing an NMP

5.4.1. Permit Terms
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5-19

NPDES Permit Writers’ Manual for CAFOs

not be necessary. However, when it is necessary to
ensure compliance with the requirements of 40 CFR part
122.42(e)(5), EPA encourages supplementing a broadly
applicable term with permit terms that are based on sitespecific information that is provided in the NMP. (For
approaches on writing the minimum NMP requirements
as permit terms, see Section 4.1.7.)
As discussed, in some instances, NRCS practice standards
can be included as part of this permit term. Table 5-2
identifies the technical basis for ensuring proper
mortality management and the NRCS conservation
practice that might address the relevant activity. Where
references are made to NRCS standards, permit writers
should ensure that necessary O&M actions are also
included as permit terms. (See Appendix K, NRCS
Conservation Practice Standards.)

Sample broadly applicable permit
language
Properly dispose of dead animals within
3 days unless otherwise provided for
by the Director. Mortalities must not
be disposed of in any liquid manure
or process wastewater system that
is not specifically designed to treat
animal mortalities. Dead animals shall
be disposed of in a manner to prevent
contamination of waters of the U.S. or
creation of a public health hazard.

Table 5-2. EPA minimum practice/NRCS Conservation practice comparison
NPDES NMP
minimum
practice
Ensure proper
management of
mortalities

Associated NRCS
conservation practice
standard

Technical basis
Improper disposal of dead animals can
result in contamination of waters of the
U.S. Nutrients and other contaminants
released from decomposing animals
can be transported to waters of the
U.S. in runoff.

Animal Mortality Facility NRCS Practice Code 316

5.4.2. Technical Information on Mortality Management
and Disposal
In confined livestock and poultry operations, animals routinely die as a result of disease, injury,
or other causes. USDA has determined typical mortality rates at livestock operations. The actual
mortality rate at an operation will depend on weather and other variables. The mortality rate
will also vary according to the age of the animal. Mortality rates are generally higher in newborn
animals. For example, a typical mortality rate for newborn pigs is 10 percent, but for older finishing
hogs, it is only 2 percent (USEPA n.d.). Table 5-3 presents typical livestock and poultry mortality
rates. The capacity for mortality storage or disposal addressed in the plan should be consistent
with those or other values typical for the CAFO’s location and operational characteristics.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.4.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-20

NPDES Permit Writers’ Manual for CAFOs

Table 5-3. Poultry and livestock mortality rates
Poultry type

Average
weight (lbs)

Mortality
rate (%)

Flock life
(days)

Design
weight (lbs)

Broiler

4.2

4.5%–5%

42–49

4.5

Layers

4.5

14%

440

4.5

Breeding hens

7–8

10%–12%

440

8

Turkey, females

14

5%–6%

95

14

Turkey, males

24

9%

112

24

Swine
growth stage

Mortality rate (%)

Average
weight (lbs)

Low

Average

High

Design
weight (lbs)

6

< 10%

10%–12%

> 12%

10

24

< 2%

2%–4%

> 4%

35

Growing-finishing

140

< 2%

2%–4%

> 4%

210

Breeding herd

350

< 2%

2%–5%

> 5%

350

Birth to weaning
Nursery

Cattle/horses
growth stage

Mortality rate (%)

Average
weight (lbs)

Low

Average

High

70–130

< 8%

8–10%

> 12%

130

Weaning

600

< 2%

2%–3%

> 3%

600

Yearling

900

< 1%

1%

> 1%

900

< 0.5%

0.5%–1%

> 1%

1,400

Birth

Mature
Sheep/goats
growth stage

1,400

Mortality rate (%)

Design
weight, (lbs)

Average
weight (lbs)

Low

Average

High

Design weight
(lbs)

8

< 8%

8%–10%

> 10%

10

Lambs

50–80

< 4%

4%–6%

> 6%

80

Mature

170

< 2%

3%–5%

> 8%

170

Birth

Source: Ohio State University Extension 1999.

Catastrophic mortality can occur when an epidemic infects and destroys the majority of a
herd or flock in a short time or when a natural disaster, such as a flood, blizzard, or tornado,
strikes. Catastrophic mortality management plans are typically expected for swine and poultry
operations because the animals confined at those operations are more susceptible to disease
outbreaks and more sensitive to extreme weather conditions than the animals confined at beef
and dairy operations. Heat waves are a particular concern for the broiler industry and are that
sector’s most common cause of catastrophic mortality.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.4.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-21

NPDES Permit Writers’ Manual for CAFOs

Animal Mortality Disposal Practices
Historically, dead animals were often taken to a remote area, where the carcasses were allowed
to decompose and be eaten by scavengers. The practice is
now illegal in virtually the entire United States because it
facilitates the spread of disease from one operation to another,
and it presents a significant risk of surface and groundwater
contamination. Mortality handling should be practiced in
accordance with all applicable state and local regulations.
CAFOs could also be required to manage mortalities consistent
with NRCS Conservation Practice Standard—Animal Mortality
Facility (Code 316). The standard establishes the minimum NRCS
requirements for the on-farm treatment or disposal of livestock
and poultry carcasses. In many cases, state or local laws and
ordinances may prohibit the use of specific animal mortality
Catastrophic cattle mortality as a result
practices, which should be reflected in the plan. Such regulations
of a blizzard. (Source: US EPA)
can often be found at the state department of agriculture or the
state or county health department.
The number of livestock mortality practices being used in the industry today is limited. The
following practices might be commonly encountered in a mortality management plan. For a more
detailed discussion on how each of the practices is implemented, see the Livestock and Poultry
Environmental Stewardship Program—Lesson 51 - Mortality Management at
http://www.extension.org/pages/8964/livestock-and-poultry-environmental-stewardshipcurriculum-lessons.
▶ Rendering—If rendering is identified in the NMP as the method for addressing animal
mortality, the NMP should specify the location on the operation where the dead
animals are to be stored for pickup and practices to ensure runoff or leachate from
the storage area is managed properly. The location of the rendering facility should be
identified, which the permit writer should verify along with the facility’s operational
status. The pickup schedule should be included. The on-site storage capabilities should
be consistent with the schedule.
▶ Composting—If composting is the method identified in an NMP to address animal
mortality, the plan should address the following:
— Frequency with which mortalities are removed from the confinement facilities
(typically that should be daily).
— How precipitation that comes into contact with the compost pile is collected or
diverted to prevent a discharge.
— Operational parameters that should be from a documented source (e.g., USDA,
land grant university).

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.4.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-22

NPDES Permit Writers’ Manual for CAFOs

— How compost is stored until it can be applied in accordance with the timing
prescribed by the NMP or prepared for sale to others.
▶ Incineration—If incineration is the method identified in the NMP to address animal
mortality, all necessary state and local permits should be identified in the plan.
▶ Sanitary landfills—If a sanitary landfill is identified as the method for addressing
animal mortality the plan should address the following:
— Name and location of the landfill.
— Operator of the landfill.
— The plan might also have to address specific transportation issues, as some states
require special licenses to transport dead animals.

Additionally, the permit writer should verify whether the landfill accepts dead
animals.

▶ Burial—If burial is the method to address animal mortality, review of the plan should
include the following:
— Documentation of any state and local siting requirements.
— An alternative method for addressing mortality when the weather precludes burial
(e.g., frozen ground).

Additionally, the permit writer should verify that burial is allowed by the operation’s
state and confirm that the location of the burial area is consistent with all siting
requirements. If a plan identifies burial as the method for addressing animal mortality,
a more comprehensive review of the plan or inspection of the facility should be
performed for the purpose of protecting against discharges to groundwater that has a
direct hydrologic connection to waters of the U.S. or to verify compliance with other
state requirements beyond NPDES if appropriate.

▶ Disposal pits—If a disposal pit is the identified method to address animal mortality,
the permit writer should take the following steps:
— Verify that the state and locality where the operation is located allow the practice.
— If there are state or local siting requirements, confirm that they have been
addressed in the NMP.
— Determine whether there are any areas of high risk to groundwater and confirm
that the disposal pit is not in those areas.

Additionally, if an NMP identifies disposal pits as the method for addressing
animal mortality, a more complete review of the plan or inspection of the
facility should be performed to ensure that no groundwater or surface water
contamination is taking place.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.4.2. Technical Information
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-23

NPDES Permit Writers’ Manual for CAFOs

With proper siting, construction, operation, and management, all those practices can be used
without significant risk to water quality. In general, however, rendering and composting when
properly implemented would be the most environmentally responsible practices. In addition,
those practices allow nutrients to be recycled. Although incineration, sanitary landfills, burial,
and disposal pits might be acceptable from a regulatory perspective, the nutrients are generally
not recycled, and each carries a greater risk to the environment. Table 5-4 identifies some of the
risks posed by those practices.
Table 5-4. Environmental risks of common mortality disposal practices
Practice

Potential environmental risks

Incineration

Incineration can release of particulates and other contaminants to the atmosphere.
Ash that remains must be properly handled and disposed of to avoid surface and
groundwater contamination.

Sanitary
landfills

Disposal in sanitary landfills can result in groundwater contamination if the facility
does not have the proper leachate control mechanisms in place.

Burial

Burial can result in groundwater contamination.

Disposal pits

Disposal pits can result in groundwater contamination.

5.5. Clean Water Diversion 40 CFR Part 122.42(e)(1)(iii)
Clean water and floodwaters that come into contact with manure have the potential to
contaminate surface water. Clean water must be diverted, as appropriate, from the production
area. Any clean water that is not diverted and comes into contact with raw materials, products,
or by-products including manure, litter, process wastewater, feed, milk, eggs, or bedding is, by
definition, process wastewater and thus is subject to the effluent limitations specified in the
permit. Where clean water is not diverted the permittee must document that it will be collected
and has been accounted for to ensure adequate storage capacity as a condition of the permit
(see Section 5.3.2). Diverting clean water from upslope areas and directing runoff away from the
production area can reduce waste volume and storage requirements. In most cases diverting
clean water is more cost-effective than providing additional storage capacity. Clean water
includes, but is not limited to, rain falling on the roofs of facilities and runoff from adjacent land.

5.5.1. Permit Terms for Clean Water Diversion
To the extent that broadly applicable permit terms meet the requirements above for ensuring
that clean water is diverted from the production area (including any necessary O&M), additional
requirements may not be necessary. However, when it is necessary to ensure compliance with the
requirements of 40 CFR part 122.42(e)(5), EPA encourages supplementing a broadly applicable
term with permit terms that are based on site-specific information that is provided in the NMP.
(For approaches on writing the minimum NMP requirements as permit terms, see Chapter 4.1.7.)
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.5.1. Permit Terms
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-24

NPDES Permit Writers’ Manual for CAFOs

Water run-off control with the use of a gutter system at a dairy in
Tillamook, Oregon. (Photo courtesy of USDA/NRCS)

Site-specific terms would identify and require implementation of conservation practices, BMPs or
engineering controls needed to exclude clean water from production areas such as the following:
▶ The construction and maintenance of perimeter controls (e.g., berms, dikes, or
channels).
▶ Installation of roof runoff management techniques (e.g., gutters, downspouts, aboveand below-ground piping).
▶ O&M procedures required to maintain the identified practices, BMPs or engineering
controls. Depending on which practices are identified and used in the NMP sitespecific O&M, terms could include the following:
— Frequency of inspection of stormwater management facilities.
— Maintenance of berm, dike or channel height.
— Removal of sediment and vegetation from channels.
— Cleaning and inspection of roof runoff controls.

Sample broadly applicable permit language
Ensure that clean water is diverted, as appropriate, from the production area. Any clean water that
is not diverted and comes into contact with raw materials, products, or by-products including
manure, litter, process wastewater, feed, milk, eggs, or bedding is subject to the effluent limitations
specified in this permit. Where clean water is not diverted from the production area, the retention
structures shall include adequate storage capacity* for the additional clean water. Clean water
includes, but is not limited to, rain falling on the roofs of facilities and runoff from adjacent land.
* Specifically addressed in terms for adequate storage capacity
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.5.1. Permit Terms
5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-25

NPDES Permit Writers’ Manual for CAFOs

Table 5-5 identifies the technical basis for diversion of clean water and the NRCS conservation
practices that could address the relevant activity and could be included as part of this permit
term. Where references are made to NRCS standards, permit writers should ensure that necessary
O&M actions are also included as permit terms.
Table 5-5. EPA minimum practice/NRCS conservation practice comparison
NPDES NMP
minimum
practice
Diversion of
clean water

Associated NRCS
conservation practice
standards

Technical basis
Clean water that comes into contact with manure
and wastewater has the potential to contaminate
waters of the U.S. Water that is not diverted is to
be collected and properly handled and stored.

Diversion - NRCS Practice
Standard Code 362
Roof Runoff Structure - NRCS
Practice Standard Code 558

5.6. Prevention of Direct Animal Contact with Waters of
the U.S. 40 CFR Part 122.42(e)(1)(iv)
BMPs must be in place to prevent the direct contact of animals confined or stabled at the facility
with waters of the U.S. in the production area. The NMP must describe how the operator will
prevent animals in the production area from coming into direct contact with waters of the U.S.,
including standing in, crossing, or drinking from such waters.

5.6.1. Permit Terms for Prevention of Direct Animal Contact
with Waters of the U.S.
To the extent that broadly applicable permit terms meet the requirements above for ensuring
that animals do not have direct contact with waters of the U.S. while in the production area
(including any necessary O&M), additional requirements may not be necessary. However, when
it is necessary to ensure compliance with the requirements of 40 CFR part 122.42(e)(5), EPA
encourages supplementing a broadly applicable term with permit terms that are based on sitespecific information that is provided in the NMP. For example, if fencing is used in the production
area to prevent confined animals from contacting a water of the U.S., the practice, fencing, the
location and any necessary O&M for the fencing could also be included as part of the site-specific
permit term. For approaches on writing the minimum NMP requirements as permit terms, see
Section 4.1.7.

Sample broadly applicable permit language
Animals confined at the CAFO must not come into direct contact with waters of the U.S.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.
5.6.1. Permit Terms

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

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NPDES Permit Writers’ Manual for CAFOs

Table 5-6 identifies the technical basis for preventing animals from directly contacting waters
of the U.S. and the NRCS conservation practice standards that might address the relevant
activity and could be included as part of this permit term. If a reference to an NRCS practice
standard is used, the permit writer should ensure that necessary required O&M requirements
are also included as permit terms. Appendix K, NRCS Conservation Practice Standards, includes
descriptions of the conservation practice standards.
Table 5-6. EPA minimum practice/NRCS conservation practice comparison
NPDES NMP
minimum
practice

Associated NRCS
conservation practice
standards

Technical basis

Prevention of
direct contact
of animals
with waters of
the U.S.

The installation of fences, barriers, or other control
devices in the production area to prevent animals
from entering waters of the U.S. reduces erosion
and prevents the direct deposition of manure into
waters of the U.S.

Fence - NRCS Practice
Standard Code 382
Access Control - NRCS
Practice Standard Code 472

5.7. Chemical Disposal 40 CFR Part 122.42(e)(1)(v)
BMPs must be in place to ensure that
chemicals and other contaminants
handled on-site are not disposed of in
any manure or stormwater storage or
treatment system unless specifically
designed to treat such chemicals or
contaminants. CAFOs commonly
use chemicals including pesticides,
hazardous and toxic chemicals, and
petroleum products/by-products.
Pesticides and other agrichemicals are
often used in agricultural production.
However, when used or disposed of
improperly or indiscriminately, they can
create a hazard and be harmful to water
and land resources, people, and animals.

Disposing of chemicals. (Photo courtesy of USDA/NRCS)

5.7.1. Permit Terms for Chemical Disposal
To the extent that broadly applicable permit terms meet the requirements above for ensuring that
chemicals are properly contained (including any necessary O&M), additional requirements might
not be necessary. However, when it is necessary to ensure compliance with the requirements of
40 CFR part 122.42(e)(5), EPA encourages supplementing a broadly applicable term with permit
terms that are based on site-specific information that is provided in the NMP, particularly in
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.7.1. Permit Terms

5-27

NPDES Permit Writers’ Manual for CAFOs

circumstances where large quantities of chemicals or particularly toxic or dangerous chemicals
are used on-site. For approaches on writing the minimum NMP requirements as permit terms,
see Chapter 4.1.7. A list of provisions that an operator can follow is presented in Table 5-7, which
could be incorporated into the permit as a site-specific term. The permit writer should place
additional restrictions in the permit where necessary.
Table 5-7. Example NMP provisions for chemical handling and disposal
All chemicals are stored in proper containers. Expired chemicals and empty containers are properly
disposed of in accordance with state and federal regulations. Pesticides and associated refuse are
disposed of in accordance with the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) label.
Chemical storage areas are self-contained with no drains or other pathways that will allow spilled
chemicals to exit the storage area.
Chemical storage areas are covered to prevent chemical contact with rain or snow.
Emergency procedures and equipment are in place to contain and clean up chemical spills.
Chemical handling and equipment wash areas are designed and constructed to prevent
contamination of surface waters, wastewater, and stormwater storage and treatment systems.
All chemicals are custom applied, and no chemicals are stored at the operation. Equipment wash
areas are designed and constructed to prevent contamination of surface waters, wastewater, and
stormwater storage and treatment systems.

Sample broadly applicable permit language
Ensure that chemicals and other contaminants handled on-site are not disposed of in any
manure, litter, process wastewater, or stormwater storage or treatment system unless
specifically designed to treat such chemicals or contaminants. All wastes from dipping
vats, pest and parasite control units, and other facilities used for managing potentially
hazardous or toxic chemicals must be handled and disposed of in a manner sufficient
to prevent pollutants from entering the manure, litter, or process wastewater retention
structures or waters of the U.S.

Other, non-NPDES, requirements might also apply to chemical handling and disposal at CAFOs,
including the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA). Under FIFRA,
pesticide labels contain information on requirements for proper chemical disposal. In addition,
some CAFOs could be required to develop Spill Prevention, Control and Countermeasure (SPCC)
plans for oil spill prevention, preparedness, and response. Such requirements might or might
not be included in a CAFO’s NMP; however, the term for chemical disposal does not include spill
response or prevention plans. Additionally, certain chemicals will enter the waste stream during
the normal course of operation at a CAFO, such as disinfectants used to wash milking parlors or
animals (e.g., foot baths), and this permit term is not intended to prohibit such practices. Rather, it
is to prohibit the dumping and disposal of chemicals in the wastewater retention structures.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.7.1. Permit Terms

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NPDES Permit Writers’ Manual for CAFOs

Table 5-8 identifies the technical basis for proper chemical disposal and the NRCS conservation
practice standards that might address the relevant activity and could be included as part of this
permit term. If a reference to an NRCS practice standard is used, permit writers should ensure
that necessary O&M actions are also included as permit terms. Appendix K, NRCS Conservation
Practice Standards, includes descriptions of the conservation practice standards.
Table 5-8. EPA minimum practice/NRCS conservation practice comparison
NPDES NMP
minimum
practice
Chemical
handling

Associated NRCS
conservation practice
standards

Technical basis
The improper handling, storage, or disposal of
chemicals at the CAFO can result in their inappro­
priate introduction into the manure, litter, or process
wastewater handling and storage system. The land
application or accidental release of manure and
waste­water can result in contamination of waters of
the U.S. Proper handling practices incorporated into
the NMP demonstrate that the CAFO is taking the
necessary actions to prevent contamination and
protect water resources.

Agrichemical Handling
Facility - NRCS Practice
Standard Code 309
Also, chemical handling
is addressed in the O&M
section of the Nutrient
Management (Code 590)
practice standard.

5.7.2. Technical Information on Chemical Disposal
Improper chemical storage and handling presents a high potential risk for polluting surface
water and groundwater, and it creates potential for chemicals to enter and contaminate manure
wastewater storage structures. Chemicals that enter manure, litter, and wastewater storage
structures can enter surface waters during land application of the manure and wastewater or
during spills or other accidental releases. Furthermore, introduction of some types of chemicals
could interfere with treatment processes in certain lagoon systems.
A CAFO’s NMP must incorporate specific actions to be taken to prevent the improper introduction
of chemicals and other contaminants into manure and wastewater storage structures or
treatment systems unless specifically designed to treat such chemicals and other contaminants.
All wastes from dipping vats, pest and parasite control units, fuels and other petroleum products,
pharmaceuticals, and facilities used to manage other potentially hazardous or toxic chemicals
should be handled and disposed of in a manner sufficient to prevent pollutants from entering the
wastewater retention structures or waters of the U.S. Although the NMP requirement addresses
only the disposal of chemicals, EPA encourages CAFOs to minimize the use of potentially
harmful chemicals and contaminants and to address in their NMPs all areas where chemicals are
stored, mixed, and loaded as well as disposal of empty chemical containers to ensure that wastes
and runoff are controlled. Chemical handling plans should consider protection of wells, water
supplies, and drainage ways that might be in or close to chemical storage and handling areas.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.7.2. Technical Information

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NPDES Permit Writers’ Manual for CAFOs

5.8. Site-Specific Conservation Practices
40 CFR Part 122.42(e)(1)(vi)
All permitted CAFOs must implement
appropriate site-specific conservation practices
to control and minimize the runoff of nitrogen
and phosphorus to waters of the U.S. For
permitted Large CAFOs (except horse, sheep,
and duck CAFOs), the ELG specifically requires
implementation of land application setbacks or
alternative practices as described below. The
CAFO regulations also require all permitted
CAFOs to include in their NMPs any additional
conservation practices that are necessary to
control nutrient runoff.
In addition to the required setback(s) or
buffer(s), the NMP may identify practices that
Restored riparian forest buffers provide protection
are implemented for purposes other than
from manure nutrients running off into ponds and the
downstream watershed. (Photo courtesy of USDA/ARS)
controlling nutrient runoff. That could include
anaerobic digesters (code 366) heavy use
area protection (code 561), or livestock shade
structures (code 717), to name a few. To ensure that those practices are not identified as permit
terms for site-specific conservation practices, NMPs should clearly identify which conservation
practices are included for the purpose of controlling nutrient runoff to surface waters.
To the extent that conservation practices that are implemented by a CAFO are necessary to
ensure proper implementation of other practices identified in 40 CFR part 122.42(e)(1), those
practices constitute a term of the NMP. That would include, for example, practices necessary to
ensure adequate storage or to satisfy protocols for land application.

5.8.1. Permit Terms for Conservation Practices
While it is common for a number of conservation practices to be included in an NMP, Large
CAFOs (except horse, sheep, and duck CAFOs) must (at a minimum) implement the 100-foot
setback or the 35-foot vegetated buffer required by the ELG, or demonstrate that the setback or the
35-foot vegetated buffer is not necessary because of the implementation of an alternative practice.
Those ELG requirements are described in more detail, in Section 5.8.2, below. Large CAFOs
must include that practice in the NMP because it is a necessary term of the permit required to
meet 40 CFR part 122.42(e)(1)(vi). While the 100-foot setback, 35-foot buffer, or other alternative
is required only of Large dairy, beef, poultry, swine, and veal calf CAFOs, it might be a helpful
starting point for the permit writer when determining appropriate BPJ conservation practice
limits for Small and Medium CAFOs and horse, sheep, and duck CAFOs. The requirement for
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.8.1. Permit Terms

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NPDES Permit Writers’ Manual for CAFOs

conservation practices at 40 CFR part 122.42(e)(1)(viii) specifically identifies setbacks and buffers
as conservation practices that are expected be included in an NMP. In addition to not applying
manure in the required setback, CAFOs should also not apply manure in the following areas or
under the following conditions:
▶ Near or in wetlands, riparian buffer areas, water resources, wells, drinking water
supplies, high slope areas, and high erosion areas.
▶ Within concentrated water flow areas (vegetated or non-vegetated) such as ditches,
waterways, gullies, swales, and intermittent streams.
▶ When the hydraulic load/irrigation water exceeds the infiltration rate of the soil.
▶ When crops are not being grown.
▶ When the ground is frozen or snow-covered.
▶ When measurable precipitation is occurring on the day of application.
The permit authority may include these types of requirements as technology-based standards.
Any other conservation practice included in the NMP should be identified as a site-specific
permit term if the practice is necessary to meet any of the requirements associated with
40 CFR part 122.42(e)(1) or if the practice influences the outcome of the field-specific risk assessment
of the potential for nitrogen and phosphorus transport from each field and, consequently, the
application rate (for a detailed discussion on the outcome of the field-specific risk assessment of
the potential for nitrogen and phosphorus transport from each field, see Chapter 6.5.1). If the NMP
includes other conservation practices that do not control the risk of nutrient runoff and do not
affect nutrient runoff, permit writers should not include those conservation practices as a term of
the permit. In general, non-nutrient control practices should be considered enhancements, rather
than provisions required for compliance with the applicable regulations, unless they actually
do affect nutrient runoff. Conversely, such practices should not be allowed if they impermissibly
facilitate runoff that is not accounted for in the NMP. Other types of conservation practices that
might be included in a CAFO’s NMP are discussed in Section 5.8.3 below.
Site-specific permit terms for this requirement should include the identification of the specific
practice(s) that are used and the location in the production area and/or land application area
(as identified in the NMP map(s) or other sources) where the conservation practice(s) are
implemented to control nutrient runoff. Where applicable, O&M should also be included as part
of the site-specific terms. Specific O&M procedures are often required for a practice to function
efficiently throughout its expected life span. NRCS conservation practice standards may include
specific O&M requirements for certain practices. For example, O&M requirements for filter strips
(code 393) include harvesting, weed control, inspection and repair after storm events, and other
procedures to maintain species composition, stand density, and functionality of the filter strip.
Where the NRCS standard does not include specific O&M requirements, the permit writer should
add these as permit terms where appropriate to do so.
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.8.1. Permit Terms

5-31

NPDES Permit Writers’ Manual for CAFOs

Permit writers should also be aware of the expected life span of conservation practices that
are incorporated as site-specific terms to ensure that the critical nutrient control practices
remain functional and effective. Table 5-9 shows the practice life span, established by NRCS at
a national level, for conservation practices that permit writers are likely to encounter in NMPs.
A conservation practice life span is the minimum time (in years) the implemented practice is
expected to be fully functional for its intended purpose(s). The established conservation practice
life spans are based on following an O&M plan developed for the practice making it a critical part
of the permit term. A one-year application life span is established for those management type
conservation practices, where practices are reapplied (other than normal O&M) annually or more
than one time on the same land to achieve its purpose(s). Each state can establish practice life
spans for its state-specific conservation practice standards.
Table 5-9. Life spans for selected NRCS conservation practice standards
Conservation practice

Code

Life span (years)

Conservation Crop Rotation

328

1

Contour Buffer Strip

332

5

Cover Crop

340

1

Filter Strip

393

10

Grassed Waterway

412

10

Irrigation Water Management

449

1

Residue and Tillage Management

329

1

345
346
Riparian Forest Buffer

346

15

Stripcropping

585

5

Terrace

600

10

Source: NRCS eDirectives, National Bulletin 450-9-8, July 28, 2009.
http://policy.nrcs.usda.gov/viewerFS.aspx?hid=25215

While some elements of conversation practices can be broadly applicable to all facilities, such
as the requirements of the ELG, EPA believes that some elements need to be site-specific to fully
meet the requirements of 40 CFR part 122.42(e)(5). That is particularly true given the importance
that many conservation practices play in determining the outcome of the risk assessment and
therefore the amount of nutrients that are to be land applied. For approaches on writing the
minimum NMP requirements as permit terms, see Chapter 4.1.5.
Table 5-10 identifies the technical basis for conservation practices to control nutrient runoff and
the NRCS conservation practice standards that might address the relevant activity and could be
included as part of this permit term. If a reference to an NRCS practice standard is used, permit
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.8.1. Permit Terms

5-32

NPDES Permit Writers’ Manual for CAFOs

writers should ensure that necessary O&M actions are also included as permit terms. Appendix K,
NRCS Conservation Practice Standards, includes descriptions of those and other related
conservation practices.
Table 5-10. EPA minimum practice/NRCS conservation practice comparison
NPDES NMP
minimum
practice
Site-specific
conservation
practices

Technical basis

Associated NRCS conservation practice standards

The implementation
of conservation
practices reduces the
velocity of runoff,
traps sediment,
absorbs nutrients and
promotes infiltration
of runoff to prevent it
from entering waters
of the U.S.

Conservation Crop Rotation – NRCS Practice Standard
Code 328
Contour Buffer Strips – NRCS Practice Standard Code 332
Cover Crop – NRCS Practice Standard Code 340
Filter Strip – NRCS Practice Standard Code 393
Grassed Waterway – NRCS Practice Standard Code 412
Irrigation Water Management – NRCS Practice Standard
Code 449
Residue and Tillage Management – NRCS Practice
Standard Codes 329, 345, 346
Riparian Forest Buffer – NRCS Practice Standard Code 391
Stripcropping – NRCS Practice Standard Code 585
Terrace – NRCS Practice Standard Code 600

5.8.2. Required Land Application Setback and Alternatives for
Large CAFOs 40 CFR Part 412.4(c)(5)
At a minimum, the ELG prohibits Large dairy, beef, poultry, swine, and veal calf CAFOs from applying manure, litter, or process wastewater closer than 100 feet to any downgradient surface water,
open tile line intake structure, sinkhole, agricultural well head, or other conduit to surface waters
except as allowed by the two alternatives discussed below. A setback is an area where manure, litter
or process wastewater is not applied, but crops can continue to be grown. A setback reduces pollution by increasing the distance pollutants in land-applied manure, litter or process wastewater has
to travel to reach surface water bodies. CAFOs can apply commercial fertilizer in the setback zone,
and can grow crops in the setback zone, but CAFOs are encouraged not to apply any form of nutrients this close to surface waters and to implement conservation practices in these areas.
CAFOs can use two alternatives to the 100-foot setback requirement in the ELG. First, the CAFO
can establish a 35-foot-wide vegetated buffer between the land application site and waters of
the U.S. Second, the CAFO can demonstrate that the setback or the 35-foot vegetated buffer is
not necessary because of implementing an alternative practice. Each of those alternatives is
described below.
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.8.2. Land Application Setbacks

5-33

NPDES Permit Writers’ Manual for CAFOs

States can require implementation of other setbacks, such
as from property lines, homes, surface waters, wells, road
rights-of-way, and public use areas. Those setbacks would
also be included in a CAFO’s NMP; however, it would be
up to the permit writer as to whether such setbacks are
included as part of the permit term for this requirement.

35-Foot Vegetated Buffer
A vegetated buffer is a permanent strip of dense, perennial
vegetation established parallel to the contours of and
perpendicular to the dominant slope of the land application
field. NRCS standards such as practice code 393 (Filter Strip)
recommend appropriate species for cover, generally native
species. If the native species include hay or alfalfa, CAFOs
can choose such species in the vegetated buffer; however,
for the area to continue to be considered vegetated, CAFOs
should not harvest it. The purpose of a vegetated buffer is
to slow the runoff from a land application site, enhance the
filtration of the runoff, and minimize the risk of nutrients
and other pollutants leaving the land application site and
reaching surface waters. CAFOs may not grow crops in
the buffer or apply manure, litter, or process wastewater
to the buffer. NRCS standards recommend appropriate
maintenance of the buffer, such as periodic sediment
removal, nutrient removal, and vegetation trimming.

Setbacks that include multiple rows of trees and
shrubs, a grass strip, combined with terraces
protect Bear Creek in Story County, Iowa.
(Photo courtesy of USDA/NRCS)

Demonstration That the Setback is Not Necessary
CAFOs can demonstrate that the setback is not necessary because it is implementing alternative
conservation practices or field-specific conditions. If an alternative practice for compliance with
the 100-foot setback is proposed, aside from the 35-foot vegetated buffer, it should be identified
in the NMP, and the CAFO must demonstrate in its permit application or NOI that the alternative
is equivalent to the 100-foot setback. Pollutant reductions of nitrogen, phosphorus, five-day
biochemical oxygen demand (BOD5) and total suspended solids (TSS) equal to or greater than the
reductions achieved by the 100-foot setback should be demonstrated. It is the CAFO that must
ultimately make the demonstration, even if the CAFO uses information generated by others. The
regulations do not prescribe how the CAFO should make the demonstration; however, in general,
CAFOs should not be allowed to use a setback less than 100 feet or a buffer smaller than 35 feet
without implementing some additional controls. A smaller setback or buffer implemented without
additional controls, or the total absence of any setback or buffer, might be insufficient to meet
the requirement in 40 CFR part 122.42(e)(1)(vi) to “control runoff of pollutants to waters of the
United States.”
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.8.2. Land Application Setbacks

5-34

NPDES Permit Writers’ Manual for CAFOs

CAFOs should not assume that meeting state BMP requirements or implementing commonly
used conservation practices will always meet the demonstration requirement. For example,
incorporation (i.e., tilling the manure into the soil) allows nutrients to make immediate contact
with soil particles and therefore minimizes certain nutrient losses. Specifically, incorporation can
reduce dissolved phosphorus runoff from manure nutrients versus allowing manure nutrients
to remain on the surface. However, incorporation increases erosion and, therefore, increases
particulate phosphorus losses. A 100-foot setback controls nutrient losses in many forms. The
demonstration of equivalency for any proposed alternative must show that the alternative does
the same. At a minimum the pollutant reductions should address the runoff, leaching and erosion
of nutrients (nitrogen and phosphorus), BOD5, and solids.
In some cases, a state could develop a list of alternative conservation practices that have been
evaluated and demonstrated to provide pollutant reductions better than the 100-foot setback.
CAFOs should check to see whether their permitting authority has collected data and information
that could be used to demonstrate that certain conservation practices provide pollutant
reductions equivalent to or better than the reductions that would be achieved by the 100-foot
setback. A state could also provide CAFOs with information or could specify suitable methods to
facilitate the CAFO’s demonstration.

5.8.3. Additional Conservation Practices Identified in the NMP
In addition to the required 100-foot setback (or compliance alternative) for Large dairy, beef,
poultry, swine, and veal calf CAFOs, other conservation practices that are necessary to minimize
the runoff of nitrogen and phosphorus to waters of the U.S. from any CAFO could be identified as
a term of the NMP. In general, any practices on which the CAFO relies for its nutrient transport
risk assessment should be included in the
NMP. For example, practices that ensure
adequate erosion control will help control
sediment-bound nutrient transport to surface
waters. Soil erosion is typically a factor used
to calculate the P-Index, a common nutrient
transport risk assessment tool. Therefore, the
elimination of any conservation practices that
control erosion losses might change a CAFO’s
field-specific risk assessment and thereby
affect the amount of additional manure
that can be land applied. The use of residue
management, such as no-till or mulch-till, is
another example of a practice that might affect
the outcome of a CAFO’s nutrient transport
Conservation filter strips are a popular practice for Illinois
risk assessment. Such practices minimize
farmers. The strips help to keep soil and nutrients out of
soil surface disturbances and, therefore,
creeks and streams and provide quality habitat for many
species of wildlife. (Photo courtesy of USDA/NRCS)
help to control erosional nutrient losses. For
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.8.3. Additional Conservation Practices Identified in the NMP

5-35

NPDES Permit Writers’ Manual for CAFOs

that reason, residue management is also considered a key
characteristic of many P-Indices and is inextricably linked
to other aspects of the NMP, specifically the risk assessment
and, thereby, rates of application. Therefore, such types of
practices should also be included as part of the site-specific
conservation practice permit term.

5.9. Manure and Soil Testing
Protocols
40 CFR Part 122.42(e)(1)(vii)
The NMP must identify protocols for appropriate testing of
manure and soil. Testing protocols for all CAFOs should
address the sampling procedures, appropriate methods of
analysis, and the required testing frequency. Large dairy,
beef, swine, poultry, and veal calf CAFOs are required
by the ELG to analyze manure at least once annually for
nitrogen and phosphorus. Soil must be analyzed at least
once every 5 years for phosphorus. 40 CFR § 412.4(c)(3).
All CAFOs must use the results of the most recent
NRCS staff and landowner measuring residue.
representative manure, litter, and process wastewater
(Photo courtesy of USDA/NRCS)
test for nitrogen and phosphorus taken within 12 months
of the date of land application when calculating the
maximum amount of manure, litter, and process wastewater to be land applied each year.
40 CFR §§ 122.42(e)(5)(i)(B), 122.42(e)(5)(ii)(D)(2). The CAFO operator may use a 5-year manure
analysis average as long as the average includes a manure analysis taken within the past 12
months. Any CAFO using the narrative rate approach for calculating maximum amounts of
manure, litter, or process wastewater to be land applied must also rely on the results of the most
recent phosphorus soil testing requirements that are in accordance with the Director-approved
protocols. 40 CFR § 122.42(e)(5)(ii)(D)(1).

5.9.1. Permit Terms for Protocols for Manure and Soil Testing
To the extent that broadly applicable permit terms meet the requirements above for identifying
protocols for appropriate testing of manure and soil, additional requirements might not be
necessary. Adequate technical standards should identify the necessary protocols for sampling
and analyzing both manure and soil. That could include the laboratories that are to be used
(e.g., laboratories listed with the Manure Testing Laboratory Certification Program (MTLCP) or
those that meet the requirements of the North American Proficiency Testing Program (NAPT)
for soil analyses), how samples should be collected (described in Section 5.9.2 below), and which
analyses (e.g. Mehlich I, Mehlich III, Olsen, Bray, or other appropriate extractions for soil samples)
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.1. Permit Terms

5-36

NPDES Permit Writers’ Manual for CAFOs

are to be used. A broadly applicable permit term
could require following those protocols that
are established in the state Director identified
technical standards.
A site-specific component is not always
necessary for this permit term as long as
sufficient details are included in the broadly
applicable terms of the permit (or technical
standards when the technical standard is used
as a broadly applicable term). However, sitespecific measures may be included as part
of the permit term if specific information is
included in the NMP that the permit writer
deems necessary to ensure compliance with the
regulatory requirement.

Figure 5-3. Sampling soil by type or condition.
Within each field, collect a separate sample
from each area that has a different type of soil
or different management history.

No NRCS conservation practices address the
relevant activity and could be included as part of this permit term because protocols are generally
developed by each state in conjunction with land grant universities. However, it is ultimately the
Director’s determination as to what is required in the technical standards.

Sample broadly applicable permit language
Manure must be analyzed at least once annually for nitrogen and phosphorus content. Soil
must be analyzed at least once every 5 years for phosphorus content. Protocols for sampling
and analyzing the sample established in the technical standards must be followed. The
results of those analyses must be used in determining application rates for manure, litter, and
process wastewater.

5.9.2. Technical information for Protocols for Manure
and Soil Testing
The following section provides an overview of sampling methods for manure and soil analysis.
Where similar information is identified in the NMP, the information can be included as part of
the permit term for identifying appropriate protocols for the manure and soil sampling.

Manure Test Protocols
Taking samples that are representative of the manure that will be land applied is critical to
obtaining an accurate manure analysis. How the manure samples are collected, the specific
number of samples and subsamples taken, what the samples are analyzed for, and approved
laboratories or methods that are to be used to perform the analyses are all a part of the protocols
for manure testing and should be identified in the technical standard for nutrient management
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

5-37

NPDES Permit Writers’ Manual for CAFOs

(Section 6.3.1). The permit writer should verify that the methods for manure analysis in the NMP are
consistent with protocols identified by the applicable nutrient management technical standards.

Manure Sampling
Proper sampling is the key to obtaining reliable manure analysis results. Accurate laboratory
procedures have little value if the sample fails to represent the manure that is to be land applied.
This section provides a brief overview of the methods employed for different types of manure
samples. Permit writers will not generally be collecting actual samples, so this section is provided
for informational purposes only. However, enforcement actions might require sample collection,
and inspectors could also be collecting samples.
Manure samples submitted to a laboratory should represent the average composition of the
material that will be applied to the field. Reliable samples typically consist of material collected
from multiple locations within a storage structure. Typically, the subsamples from different
locations in a storage structure are mixed well, and a single sample is removed from the composite
for analysis. Representative sampling methods vary according to the type of manure. It is important that proper containers are used and maximum holding or shipping times are also identified
and followed to avoid contaminating or altering the collected samples. General sampling recommendations follow. It is always best to check with the laboratory that will analyze the samples to
know how to best prepare and ship samples and when the laboratory is willing to receive them.

Liquid manure
Liquid manure samples submitted for analysis are generally placed in a sealed, clean plastic
container with about a one-pint volume. Glass is not suitable because it is breakable and could
contain contaminants. At least 1 inch of air space is generally left in the plastic container
to allow for expansion caused by the release of gas from the manure material. Samples that
cannot be shipped on the day they are collected
should be refrigerated or frozen to minimize
chemical reactions and pressure buildup from
gases. Ideally, liquid manure should be sampled
after it is thoroughly mixed, but because that is
sometimes impractical, samples can also be taken
in accordance with the suggestions that follow.

Liquid storage effluent
Premixing the surface liquid in the liquid
storage is not needed, provided it is the only
component that is being pumped. Growers
with multistage systems should draw
samples from the liquid storage they intend
to pump for crop irrigation. Samples should
be collected using a clean, plastic container.
One pint of material should be taken from

Water samples from filtration lagoon.
(Photo courtesy of USDA/NRCS)

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

5-38

NPDES Permit Writers’ Manual for CAFOs

at least eight sites around the lagoon and then mixed in a larger clean, plastic container.
Effluent should be collected at least 6 feet from the lagoon’s edge at a depth of about one
foot. Shallower samples from anaerobic lagoons might be less representative than deep
samples because oxygen transfer near the surface sometimes alters the chemistry of the
solution. Floating debris and scum should be avoided. One pint of mixed material should be
sent to the laboratory. Galvanized containers should not be used for collection, mixing, or
storage because of the risk of contamination from metals (e.g., zinc) in the container.

Liquid slurry
Manure materials applied as a slurry from a pit or storage pond should be mixed before
sampling. Manure should be collected from several areas (approximately 8) around the pit
or pond and mixed thoroughly in a clean plastic container. An 8- to 10-foot section of 0.5to 0.75-inch plastic pipe can also be used to collect a representative sample by extending
the pipe into the manure, pressing a thumb over the end of the pipe to form an air lock,
removing the pipe from the manure, and releasing the air lock to deposit the manure in the
plastic container.
Lagoon sludge
It is somewhat more difficult to obtain a representative sample of lagoon sludge. Two
common methods are used. One method requires pumping the lagoon down to the sludge
layers. Then, during sludge agitation, a liquid or slurry type of sample described above can
be collected. The other method requires inserting a probe to the bottom of the lagoon to
obtain a column of material. A sludge-judge is a device commonly used for such sampling.
The sludge component of the column is released into a clean plastic bucket, and samples
are likewise collected from several (12 to 20) other sampling points around the lagoon to
obtain a composite, representative sample. That procedure should be performed with a
boat or mobile floating dock. For analysis, most laboratories require at least one pint of
material in a plastic container. The sample should not be rinsed into the container because
doing so dilutes the mixture and distorts nutrient evaluations. However, if water is typically
added to the manure before land application, a proportionate quantity of water should be
added to the sample.

Solid manure
Solid manure samples should represent the manure’s average moisture content. A one-quart
sample is typically adequate for an analysis. Samples are generally taken from several different
areas (approximately eight) in the manure pile, placed in a clean plastic container, and thoroughly
mixed. Approximately one quart of the mixed sample should be placed in a plastic bag, sealed, and
shipped directly to the laboratory. Samples stored for more than 2 days should be refrigerated.

Sampling within dry litter houses
Litter can be sampled in production houses before litter cleanouts, but one must take care
to collect a representative sample. Ten to fifteen small samples are typically collected from
each house and placed in a clean plastic bucket. Samples should be taken to the depth of
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

5-39

NPDES Permit Writers’ Manual for CAFOs

cleanout, being careful not to dig into the dirt floor. Cake litter samples should be taken at
the depth of cake removal. Litter samples from brooder breeder slat houses should be taken
after the slat manure and litter are mixed during the cleanout process. Material that will be
applied to the field should be sampled (e.g., cake out results should not be used to represent
total cleanout). Samples should be thoroughly mixed in the bucket. Approximately one
quart of material should be placed in a plastic freezer bag or wide-mouth plastic bottle
before submitting for analysis.

Poultry below-house manure sampling
In a high-rise system, manure is deposited below the poultry house. If the system is
properly managed, the manure should be fairly uniform in moisture and appearance.
Several (approximately eight) samples should be collected throughout the storage area. If
manure in certain areas differs in appearance, 10 percent of the manure samples should
be taken from an area that is different from the bulk of the pile. The collected material
should be combined in a plastic container and mixed thoroughly. The one-quart laboratory
sample should be taken from the mixture, placed in a plastic bag, sealed, and shipped to
the laboratory for analysis. If the sample cannot be shipped within one day of sampling, it
should be refrigerated.
Stockpiled manure or litter
Ideally, stockpiled manure and litter should be stored under cover on an impervious
surface. The weathered exterior of uncovered waste might not accurately represent the
majority of the material. Rainfall generally moves water-soluble nutrients down into the
pile. If an unprotected stockpile is used over an extended period, it should be sampled
before each field application. Stockpiled manure should be sampled at a depth of at least
18 inches at six or more locations. The collected material should be combined in a plastic
container and mixed thoroughly. The
one-quart laboratory sample should
be taken from the mixture, placed in a
plastic bag, sealed, and shipped to the
laboratory for analysis. If the sample
cannot be shipped within one day of
sampling, it should be refrigerated.
Surface-scraped manure
Surface-scraped and piled materials
should be treated like stockpiled
manure, using the same procedures
for taking samples. Ideally, surfacescraped materials should be protected
from the weather unless they are used
immediately.

Fresh manure samples collected at a swine facility near
Peoria, Illinois. (Photo courtesy of USDA/ARS)

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

5-40

NPDES Permit Writers’ Manual for CAFOs

Composted manure
Ideally, composted manure should be stored under cover on an impervious surface.
Although nutrients are somewhat stabilized in such materials, some nutrients can leach
out during rains. When compost is left unprotected, samples should be submitted to the
laboratory each time the material is applied to fields. Sampling procedures are the same as
those described for stockpiled waste.

Manure Analysis2
Both public and private laboratories analyze manure samples. Public laboratories generally
operate in conjunction with either a state land grant university or a state agricultural or
environmental agency. Private laboratories can be found through local Cooperative Extension
Service agents, the land grant university, state regulators, or other producers. State technical
standards should identify state-approved laboratories or laboratory procedures or both to
properly analyze manure. The permit writer
should ensure that any laboratory used by an
What Forms of Nutrients Should Be
operator and identified in a CAFO’s NMP has
Tested?
been selected in accordance with the state’s
At a minimum, CAFOs should test for total
technical standards.
Manure analysis results can be presented in a
number of ways. The most common way is wet,
as-is basis in pounds of nutrient (nitrogen or
phosphorus) per ton; pounds per 1,000 gallons of
manure or wastewater; or pounds per acre-inch
of manure or wastewater. If a laboratory reports
results on a dry basis, the moisture content
of the manure must be known to convert the
results back to a wet basis. A laboratory might
also give results as a concentration (parts per
million [ppm], percent (%), or milligram per liter
[mg/L]), which likewise requires conversion
factors to get the results into a usable form
according to how the manure will be applied.
Finally, if a laboratory reports phosphorus as
elemental phosphorus, it must be converted to
the fertilizer basis of P2O5. That can be done with
the following conversion:

Kjeldahl nitrogen (TKN), ammonia, total
phosphorus, and soluble phosphorus.

Organic forms of nitrogen are converted to
inorganic forms of nitrogen during a process
called mineralization. The inorganic forms
of nitrogen are used by plants. Inorganic
nitrogen, such as ammonium N (NH4+), is
usually attached to soil particles until used
by the plants. In contrast, the nitrate form
(NO3-) is highly susceptible to leaching and
can leach before used by the plant.
Adsorbed phosphorus is considered
unavailable for plant growth. Erosion and
runoff are common ways in which adsorbed
phosphorus can transport off-site and
contaminate surface water. In contrast,
highly permeable soils, low pH, and low
organic matter allow phosphorus to leach.

P × 2.29 = P2O5
Nitrogen is typically reported as total Kjeldahl nitrogen (TKN), ammonium N (NH4-N), and
sometimes nitrate-nitrogen (NO3-N). TKN is the concentration of ammonium and organic
nitrogen. NH4-N and NO3-N are directly provided by the manure analysis and are both plant
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

5-41

NPDES Permit Writers’ Manual for CAFOs

available fractions of nitrogen (for information
on plant-available nutrients, see Appendix A,
Basic Soil Science and Soil Fertility). A fraction
of the organic nitrogen will become rapidly plant
available when land applied, and additional
nitrogen will become available over the course
of the following few years. Such a release of plant
available nitrogen occurs through mineralization,
which must be accounted for when calculating
land application rates. From the manure analysis,
organic nitrogen can be calculated as the
difference between the TKN and NH4-N.

Calculating the Dry Weight of
Nitrogen in Manure
The CAFOs most recent manure sample
analysis indicates that the nitrogen
content in lb/ton wet weight is 3.3, and
the moisture content is 33 percent. To
calculate the amount of nitrogen in lb/
ton dry weight, the CAFO uses the
following equation:
Concentration N dry basis =
Concentration N wet basis × (100 G %
moisture content)

NH4-N is subject to volatilization losses. Significant
volatilization losses can occur during manure
storage; therefore, the manure analysis should
take place as close to the time of application as
possible to accurately assess the nutrient content
just before field application.

= 3.3 lb/ton × (100 G 33%)

= 2.2 lb/ton

NO3-N is not always reported in a manure analysis. Nitrate becomes available from the oxidation
of ammonium (nitrification). Manure on many animal operations is stored in an anaerobic
environment, and for those operations, measures of NO3-N are negligible. However, if manure
is stored in an aerobic lagoon or sampled from a compost source, an NO3-N analysis should be
requested.
Reports of analysis on an as-is basis should be in the units of measure and nutrient forms most
useful to an operation for nutrient planning purposes. The most useful nutrient form reported in a
manure analysis is predicted nutrients available for the first crop in a planned crop rotation. First
year nutrient availability is predicted on the basis of estimates of manure breakdown and nutrient
loss because of application method.
To meet a specific plant nutrient requirement, nutrients listed in the report or calculated as
available for the first crop should be used in determining the actual application rate. For the
availability prediction to be reliable, the person who collected the sample should have properly
identified the type of manure and the application method on the information sheet submitted to
the laboratory. All information required by the laboratory must be reported for the laboratory to
do the appropriate analysis. Sampling and shipping procedures must be followed for the results
to be accurate. It is important to understand that nutrient availability cannot be determined with
100 percent accuracy. Many variables, including the type of manure and environmental factors
(e.g., soil type, rainfall, temperature, and general soil conditions) influence the breakdown of
manure and nutrient loss.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

5-42

NPDES Permit Writers’ Manual for CAFOs

A Sample Manure Analysis. A laboratory will generally provide findings in concentration and
as a wet basis. Concentration is reported in the percent or ppm of specific constituents, while wet
basis is reported in pounds per ton, pounds per 1,000 gallons of manure/wastewater, or pounds
per acre-inch manure/wastewater for specific constituents. Below is an example of a typical
analysis report.

Soil Test Protocols
Crop nutrient requirements vary depending on factors such as soil characteristics and previous
fertilization. Soil testing is used to provide agronomic and environmentally sound nutrient and
lime recommendations. It provides growers a means to assess soil pH and plant-available nutrient
content, to determine the need for addition
of lime and nutrients, and to minimize
nutrient losses to the environment from overapplication.

Soil sampling - collection of a soil core. (Photo courtesy of
USDA/MO NRCS)

Good animal manure management includes
routine soil sampling on every field on which
manure is applied. EPA generally considers
soil sampling for phosphorus every 5 years as
the minimum necessary to properly manage
soil nutrient levels (as is required for Large
dairy, beef, poultry, swine, and veal calf
CAFOs under the ELG. 40 CFR § 412.4(c)(3).
States should consider more frequent
testing, especially for operators who are
implementing nitrogen-based NMPs.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

5-43

NPDES Permit Writers’ Manual for CAFOs

Soil Sampling
Proper sampling is the most important component of an
accurate soil test. If a representative sample is not collected,
the recommendations developed by the laboratory will likely
be inaccurate, resulting in excessive nutrient application or
deficiencies that will affect production. Permit writers and
inspectors will generally not be collecting soil samples, so this
section is provided for informational purposes only. However
enforcement actions might require the soil sample collection in
some cases.

Soil Sampling
ANSI GELPP 0004-2002, Manure
Utilization (ANSI 2002) standard
recommends sampling soils every
3 years and analyzing them for, at
minimum, nitrate content, available
phosphorus content, pH, and
buffer pH. EPA also recommends
periodically analyzing the soil
sample for nitrogen, potassium, pH,
alkalinity, metals, micronutrients,
and organic matter to better
assess the soil conditions at a land
application site.

Every soil sample submitted for testing typically consist of about
15 to 20 cores taken at random locations throughout one field
or management unit. The various cores will be used to form one
composite sample to be submitted for laboratory analysis. Keep
in mind that each composite sample should represent only one
general soil type or condition (see Soil Surveys text box). If the field
contains areas that are obviously different in slope, color, drainage,
and texture and if those areas can and will be managed separately, a separate sample should be
submitted. Many state technical standards will establish a maximum field acreage that a soil
sample can represent; it is important for a permit writer to be aware of those limits.

Soil Surveys
Planners and permit writers can use published soil surveys to identify fields or sub-fields that should
be sampled or managed separately on the basis of variations in soil type. The National Cooperative
Soil Survey (NCSS), coordinated by NRCS, is a county-by-county scientific inventory of U.S. soils on
nearly all public and private land.
Soil surveys contain soil maps and general information about the agriculture and climate of the
area and descriptions of each soil type. A soil survey could also include interpretations of the soil’s
characteristics, and guidance for community planning, agricultural land management, engineering,
and wildlife management.
Soils in the survey are classified by soil orders, suborders, great groups, subgroups, families, and
series. The U.S. system of soil classification recognizes approximately 15,000 different soil series.
Soil survey reports are available from several sources.
• The state or local NRCS office, county extension office, or congressional representatives
might offer free reports.
•

Public libraries and conservation district offices generally have reference copies available.

•

Soil surveys are available on the Web Soil Survey website: http://websoilsurvey.nrcs.usda.gov

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

5-44

NPDES Permit Writers’ Manual for CAFOs

When collecting soil samples, small areas where the soil conditions are obviously different from
those in the rest of the field should be avoided; examples include wet spots, old manure and urine
spots, places where wood piles have been burned, severely eroded areas, old building sites, fence
rows, spoil banks, and the like. Samples taken from such locations are not typical of the soil in
the rest of the field, and including them could produce misleading results. Areas in a field where
different crops have been grown in the past should be sampled separately even if the same crop
will now be planted in the entire field. Areas that have been limed and fertilized differently from
the rest of the field should also be sampled separately.
To avoid contamination of the samples, samples should be collected with stainless steel or
chrome plated sampling tools and plastic buckets. Brass, bronze, or galvanized tools should
be avoided. Tools and buckets should be clean and free of lime and fertilizer residues. Even a
small amount of lime or fertilizer transferred from the sampling tools to the soil can seriously
contaminate the sample and produce inaccurate results.
For soil samples intended for analysis of phosphorus and other immobile nutrients (potassium,
calcium, and magnesium), samples should be collected at the same depth to which the
field is tilled (usually about 6 to 8 inches) because that is the zone in which the fertilizer has
been incorporated. For fields that rely on no-till management, non-mobile nutrients such as
phosphorus become stratified. Phosphorus can become concentrated within the 0- to 2-inch
depth and depleted at lower soil depths. Sampling procedures should be adjusted to identify
variation of nutrient availability that can change under different types of land management
so that recommendations can be adjusted. For areas that use soil nitrate testing, a deeper core
sample might be needed. It is important to collect soil samples from the depth specified by the
permit or technical standards. Those sources might refer to recommendations provided by the
approved laboratory to which the sample will be sent for analysis. Before filling the shipping
container, the cores should be pulverized and mixed thoroughly in a clean, plastic bucket. The
composite soil samples should be air dried and the shipping container filled about two-thirds full
with the mixture. Once the soil test results are known, the final fertilizer and lime suggestions
can be made. Recommendations are typically given on a per-acre basis for each nutrient.

Soil Analysis
A soil test is a laboratory procedure that measures the plant-available portion of soil nutrients.
The measurement is used to predict the amount of nutrients that will be available during the
growing season. In general, the soil test is an extraction procedure that has been tailored to a
specific region.3 A soil test is used to assess the fertility of a soil but does not provide a direct
measure of the actual quantity of plant available soil nutrients. Therefore, a soil test is used to
predict a crop response and can be used to provide a nutrient recommendation needed to achieve
a given crop response.
Soil tests provide quantitative and qualitative analyses regarding the availability of nutrients
in the soil. A single quantitative numeric value is provided, which is interpreted on the basis

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

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NPDES Permit Writers’ Manual for CAFOs

of regional crop response research. The
quantitative value is typically given in ppm or
pounds per acre (lbs/A) elemental phosphorus,
potassium, magnesium, or any other element
that is being analyzed. Interpretation of the soil
test value is based on the current availability
of the nutrient being analyzed in the soil.
Interpretations typically range from very low
to very high or excessive. Interpretations have
also been described using the terminology
optimum and below or above optimum. The
way categories are described and the number
of categories that are defined is typically
determined by the land grant universities or the
soil testing laboratory.
Nutrient levels designated optimum (or in
some states medium or high) indicate sufficient
levels of plant available soil nutrients for a given
crop yield. Soil test levels designated very high
or excessive indicate more-than-sufficient
availability of soil nutrients for plant growth.
Soil samples examined in a lab.
The qualitative categories describing a soil test
(Photo courtesy of USDA/MO NRCS)
(e.g., low, medium, optimum, high, very high,
excessive) can generally be compared state to
state across similar geographic regions because they describe whether an increase in yield can be
expected if additional nutrient is applied. However, the quantitative values defining each category
will differ depending on the soil test method used for the nutrient extraction, regional growth
range ratings, and numeric standards for each range which are set by each state.
Laboratories will use different extracting solutions and methods for analyzing nutrient
availability. That is mainly because different extractants are more appropriate for different
soil properties, which vary across regions. A good example of this is the analysis used for
soil phosphorus. The Mehlich 1, Mehlich 3, Morgan, and Modified Morgan extractants are
predominant in the northeastern United States. Since the chemistry of northeastern soils
primarily involves factors affecting the availability of aluminum phosphates, soil tests in the
northeast use a dilute acid solution to dissolve these minerals and extract phosphorus. The
Mehlich III extracting solution can be used across a wider variety of soils, including calcareous
soils, whereas the Mehlich I extraction solution is not as effective for such types of soils.
Laboratories also report results using different units. Commonly, results are expressed as lbs/A,
ppm, or as a fertility index value. Given those variations, it is very difficult to convert analyses.
It is most important to follow the recommendation developed by the laboratory for the sample
analyzed.
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

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NPDES Permit Writers’ Manual for CAFOs

Nitrogen
Not all laboratories test for soil nitrogen. It is a very mobile nutrient in the environment, and
soil levels can change rapidly in a short period. For laboratories that do nitrogen testing, it is
important to remember that the sampling depth for nitrogen might be different from that for
other analyzed components (phosphorus, potassium, or pH) and that the nitrogen test is only
relevant if a sample can be obtained, analyzed, and reported back to the producer in a short
period. Nitrogen sampling in this mode is very valuable and saves money by reducing fertilizer
costs and environmental risks.

Pre-Sidedress Soil Nitrate Test (PSNT)
The PSNT is a widely used tool for optimizing nitrogen fertilizer use efficiency
for corn production. The test relies on timely measurement of mineralized
soil nitrate in the top layer of soil just before corn’s period of rapid nitrogen
uptake. The PSNT is highly recommended for corn fields where manure (and
other organic sources of nitrogen) has been applied recently. The PSNT may
be less reliable when total nitrogen application before sidedress exceeds
50 pounds nitrogen per acre. CAFOs should consult their local Extension
Service for more information.

Phosphorus
Phosphorus is an essential nutrient for crop and animal production, but it can accelerate
freshwater eutrophication—one of the most common water quality impairments. Because
phosphorus is relatively stable in soils, soil testing is useful for determining the relative levels of
phosphorus available to crops, monitoring phosphorus accumulation over time, and determining
when soil phosphorus levels are high enough that no additional land application is necessary.

Soil Phosphorus Test
A soil sample from the site is necessary to assess the level of available
phosphorus in the surface layer of the soil. The available phosphorus is the
level customarily given in a soil test analysis by the Cooperative Extension
Service or commercial soil test laboratories. These ranges of soil test
phosphorus values will vary by soil test method and region. The soil test
level for available phosphorus does not ascertain the total phosphorus in
the surface soil. It does, however, give an indication of the amount of total
phosphorus that might be present because of the general relationship
between the forms of phosphorus (organic, adsorbed, and labile phosphorus)
and the solution phosphorus available for crop uptake.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.9.2. Technical Information

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NPDES Permit Writers’ Manual for CAFOs

5.10. Protocols for Land Application
40 CFR Part 122.42(e)(1)(viii)
The requirements for addressing the protocols for land application are discussed in depth in
Chapter 6.

5.11. Recordkeeping
40 CFR Parts 122.42(e)(1)(ix) and (e)(2)
The NMP must identify the records that will be kept to document implementation of all
NMP minimum requirements, including the records specified for O&M. The records must
be maintained on-site. 40 CFR § 122.42(e)(2). Section 4.2.2 describes the record-keeping
requirements included in the CAFO rule, including the ELG record-keeping requirements for
Large CAFOs. Table 5-11 includes examples of the types of site-specific records that a CAFO might
include in its NMP to document implementation of the nine minimum NMP requirements.
Table 5-11. Example site-specific records to document NMP implementation
NMP
minimum
requirement

Example site-specific records

Ensure
adequate
storage

• Dates of weekly visual inspections of Ponds A, B, and C, including the exposed
portion of the pond liners; the south swale to Pond A; the east swale to Pond C;
and Pumps 1 and 2 (Weekly Records form)
• Description of deficiencies and corrective actions associated with weekly
inspections (Weekly Records form)
• Weekly records of the wastewater level in Ponds A, B, and C (Weekly Records
form)
• Daily precipitation records (Rain Gauge log form)
• Document daily inspections of the east and west drinking water lines, the central
cooling line, and the piping from the well to the barn (Weekly Records form)
• Monitor Pumps 1 and 2 hourly during all wastewater applications (Wastewater
Application Log form)
• Dates of solids/sludge removal from Ponds A, B, and C

Ensure proper
management
of mortalities

• Monthly documentation (initial) that all dead animals were handled and
disposed of as described in the NMP (Monthly Records form)
• Renderer invoices (electronic copies stored on computer)
• For catastrophic mortality, document the number, average weight, cause, and
date of animal deaths and the method of disposal.

Diversion of
clean water

• Dates of weekly visual inspections of the north and west berms (Weekly Records
form)
• Dates of weekly visual inspections and cleaning/repair as needed of gutters,
downspouts, and underground piping for roof runoff (Weekly Records form)

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5-48

NPDES Permit Writers’ Manual for CAFOs

Table 5-11. Example site-specific records to document NMP implementation (continued)
NMP
minimum
requirement

Example site-specific records

Prevention of
direct contact
of animals
with waters of
the U.S.

• Records of visual inspections of the east perimeter fencing along Spring Creek,
at a minimum monthly and after storms and other disturbance events (Monthly
Records form)
• Description of deficiencies and corrective actions associated with visual
inspections (Monthly Records form)

Chemical
disposal

• Maintain inventory of chemicals stored or handled at the facility.
• Date of monthly inspections of the chemical storage shed, including a
description of conditions that would cause concern, and required actions as
appropriate (Monthly Records form)
• Monthly documentation (initial) that all chemicals were handled and disposed of
as described in the NMP (Monthly Records form)
• Dates of employee training and names of employees trained on proper chemical
handling and disposal

Conservation
practices
to control
nutrient loss

• Document implementation of mowing and maintenance schedule for Field 15
and 15a buffer strip including monitoring of vegetative density, reseeding, and
redistribution of sediment as needed (Monthly Records form)
• Document inspections of the Field 24 filter strip at a minimum monthly
and after storm events, including repair of any gullies that have formed,
removal of unevenly deposited sediment accumulation that will disrupt sheet
flow, reseeding of disturbed areas and other measures necessary to prevent
concentrated flow through the filter strip (Monthly Records form)

Protocols for
manure and
soil testing

• Sampling dates and results of soil analyses for all fields (ensure laboratory reports
identify methods of analysis)
• Sampling dates and results of irrigation water nutrient analyses
• Sampling dates and results of manure analyses, east and west stockpiles (ensure
laboratory reports identify methods of analysis)
• Sampling dates and results of wastewater analyses, Ponds B and C (ensure
laboratory reports identify methods of analysis)

Protocols
for land
application of
manure and
wastewater

• Complete Wastewater Application Log form for each land application event on
each field, including
• Calculations showing the total N (PAN) and P (P2O5) to be applied (complete
before land application)
• Total amount of PAN and P2O5 actually applied, including calculations
• Weather conditions 24 hours before application, at the time of application, and
24 hours after application
• Document dates of inspections of Pumps 1 and 2 and all piping used to transfer
wastewater from Ponds B and C to each field, and the center pivots irrigators on
each field (minimum once annually and daily during application)

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

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NPDES Permit Writers’ Manual for CAFOs

The requirement for record keeping can be established
in the general permit as a broadly applicable permit
condition by specifically identifying all the records
required to be maintained by all CAFOs covered
under the permit. A site-specific component is not
required as part of the permit term; however, sitespecific measures may be implemented if necessary
and included in the NMP. A permit writer could
determine that some of the site-specific records
identified in the NMP are necessary to ensure
implementation of the minimum NMP requirements
and include them as site-specific terms in the permit.
Moreover, the permit writer might determine that
certain site-specific measures require site-specific
records, even if those records are not identified in the NMP. The specific record-keeping
requirements of the CAFO rule are described in Chapter 4.2.2.

5.12. Developing an NMP
5.12.1. USDA’s Comprehensive Nutrient Management Plan
A comprehensive nutrient management plan (CNMP) is a plan developed according to standards
established by USDA’s NRCS to manage manure and organic by-products by combining
conservation practices and management activities into a conservation system that, when
implemented, will protect or improve air, soil, and water quality. The CNMP need not be a
document separate from the NMP required by the CAFO regulations. The NMP minimum
requirements in the CAFO regulations were developed to be consistent with the content
of a CNMP as defined by USDA policy and CNMP Technical Criteria. The NMP minimum
requirements represent a subset of the management practices and activities that would generally
be included in a USDA-defined CNMP. The content of a USDA-defined CNMP is described in the
USDA policy and CNMP Technical Criteria (for website links, see Appendix N, References for
NPDES Permit Writers). Table 5-12 identifies each of the 10 elements of a CNMP and indicates
which of the NMP minimum requirements for CAFOs would typically be addressed under each
element during the development and implementation of a CNMP.
There are some situations where the CNMP might not fully address all the EPA NPDES minimum
requirements. For example, the CNMP technical guidance does not specifically include the
prevention of direct contact of animals with waters of the U.S. within the elements of a CNMP.
However, the prevention of direct contact is strongly recommended through the CNMP technical
criteria and in the Nutrient Management 590 conservation practice standard (USDA-NRCS 2006)
and is generally considered to be a component of the conservation planning process. The CNMP
is defined by USDA as a part of the conservation planning process focused on AFOs. If the CNMP

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP
5.12.1. USDA’s Comprehensive NMP

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NPDES Permit Writers’ Manual for CAFOs

does not fully address the minimum requirements required by the CAFO regulation, it cannot
qualify as a valid NMP for use with an NPDES CAFO permit. It is important to bear in mind that an
NMP must meet all the requirements established by the Director (and discussed in this manual).
For a CNMP to qualify as an NMP for NPDES permitting, it will need to satisfy those conditions.
EPA’s NPDES NMP minimum requirements do not address two of the ten elements of USDA’s
CNMP—Feed Management and Other Utilization Options. Although those are important and
should be considered in the development of a site-specific CNMP or NMP for CAFOs, they do not
have to be addressed, as regulatory requirements, in NMPs developed as condition of a CAFO’s
NPDES permit.
Table 5-12. USDA CNMP elements/NPDES NMP minimum practices comparison
USDA CNMP elements

NPDES NMP minimum practices

Background and Site Information
Manure and Wastewater Handling
and Storage

Adequate storage capacity

Farmstead Safety and Security

Chemical handling

Diversion of clean water
Prevention of direct contact of animals with waters of the U.S.
Mortality management

Land Treatment Practices

Conservation practices to control nutrient loss

Soil and Risk Assessment Analysis

Protocols for the land application of manure and wastewater

Nutrient Management

Protocols for the land application of manure and wastewater
Protocols for manure and soil testing

Record Keeping

Record keeping

Feed Management
Other Utilization Options
References

5.12.2. Technical Assistance for Preparing NMPs
EPA anticipates that permitting authorities will coordinate with their state agricultural agency
partners to prepare guidance on implementing the established state nutrient management
technical standard when developing the site-specific NMP required by the permit. (For additional
information on the requirements of a technical standard, see Chapter 6.3.1.) In addition, a CNMP
prepared in accordance with the CNMP Technical Criteria issued by USDA’s NRCS should meet
most of the NMP and minimum practice requirements of the permit. (To review NRCS’s CNMP
Technical Criteria, see NRCS National Instruction 190-304.)

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.12.2. Technical Assistance for Preparing NMPs

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NPDES Permit Writers’ Manual for CAFOs

Nutrient Management Planning Tools
Many states, universities, and private sector companies have developed nutrient management
tools that can be used (generally within a specific state) to assist livestock and poultry
producers develop site-specific NMPs. One example of such tools follows:
Manure Management Planner (MMP): Developed at Purdue University; a manure utilization
planning tool to help develop NMPs. You can access MMP at http://www.agry.purdue.edu/mmp/
Appendix L, Nutrient Management Planning Software, provides additional information on
other state software programs available for generating NMPs.

CAFO owners and operators should seek technical assistance for developing NMPs. Federal
agencies, such as the NRCS, and state and tribal agricultural and conservation agency staff,
Cooperative Extension Service agents and specialists, Soil and Water Conservation Districts,
and land grant universities might be able to provide technical assistance. Producers might also
be able to obtain information from industry associations, integrators and private consultants.4
A number of computer-based tools are being developed to facilitate the development and
implementation of NMPs. (For a discussion on available software programs, see Appendix L,
Nutrient Management Planning Software.)

5.12.3. NMPs Developed by Certified Specialists
Although EPA’s CAFO regulations do not require CAFOs to use a certified specialist or technical
service provider to develop the required site-specific NMP, permitting authorities should
encourage and support the use of the specialists. If a CNMP is used to meet the nutrient
management requirements when seeking NPDES permit coverage, the CNMP would have
to be signed by a certified specialist because that is a requirement for all CNMPs. A certified
specialist is a person who has demonstrated
capability to develop NMPs in accordance
with applicable USDA or state standards and
is certified by USDA or a USDA-sanctioned
organization. Certified specialists include
qualified persons who have received
certifications through a state or local agency,
personnel from NRCS, and persons who
have completed technical service provider
certification programs recognized by NRCS
or other programs recognized by states. In
addition, USDA has developed agreements
with technical service providers to provide
certified NMP development services. Thirdparty vendor certification programs could
A producer and NRCS staff members work together.
include (1) American Society of Agronomy’s
(Photo courtesy of USDA/NRCS)
5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.12.3. NMPs Developed by Certified Specialists

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NPDES Permit Writers’ Manual for CAFOs

certification programs, including Certified Crop Advisors and Certified Professional Agronomists,
Certified Professional Crop Scientists, and Certified Professional Soil Scientists; (2) land grant
university certification programs; (3) National Alliance of Independent Crop Consultants; and
(4) state certification programs.
An NMP preparer certification program is one mechanism that a state can use to ensure that
plans are prepared in accordance with the nutrient management technical standard established
by the Director. Many states have the discretion to require their use to prepare or approve plans.
EPA recognizes that some states could require NMPs to be certified under state requirements. The
value of using certified specialists is to ensure that NMPs are developed, reviewed, and approved
by persons who have the appropriate knowledge and expertise to ensure that plans fully and
effectively address the applicable ELG requirements, the minimum practices, and the applicable
state nutrient management technical standard and are appropriately tailored to the site-specific
needs and conditions of the CAFO. Because of the multidisciplinary nature of NMPs, it is likely
that a range of expertise will be needed to develop an effective NMP (e.g., professional engineer,
crop specialist, soil specialist).

References
ANSI (American National Standards Institute). 2002. Good Environmental Livestock Production
Practices: Concentrated Livestock Operations – Manure Utilization 004-2002. American
National Standards Institute, Washington, DC.
Fulhage, C.D. 2000. Laboratory Analysis of Manure. Reviewed and reprinted 6/00/7M.
Environmental Quality MU Guide. University of Missouri Extension, Columbia, MO.
.
Harrison, J.D. and D. R. Smith. 2004a. Annual Manure Removal Methods for Manure Storage
Facilities. Agriculture Environmental Management Systems. Utah State University Extension,
Logan, UT. .
Harrison, J.D. and D. R. Smith. 2004b. Lagoon Monitoring and Condition Parameters. Agriculture
Environmental Management Systems. Utah State University Extension, Logan, UT.
.
Ohio State University Extension. 1999. Ohio’s Livestock and Poultry Mortality Composting Manual.
Ohio State University Extension, Columbus, OH.
USDA (U.S. Department of Agriculture). 2009. General Manual. Title 190 – Part 405
Comprehensive Nutrient Management Plans and National Instruction- Comprehensive
Nutrient Management Plans Technical Criteria (NI-190-304). U.S. Department of Agriculture,
Washington, DC. . Accessed November 1, 2011.

5. Nutrient Management Planning
5.1. Nine Minimum
Requirements

5.2. Developing Permit
Terms

5.3. Adequate Storage

5.4. Mortality Management

5.5. Clean Water
Diversion

5.6. Prevention of Direct Animal
Contact with Waters of the U.S.

5.7. Chemical Disposal

5.8. Conservation Practices

5.9. Manure and Soil Testing

5.10. Protocols for Land
Application

5.11. Recordkeeping

5.12. Developing an NMP

5.12.2. Technical Assistance for Preparing NMPs

NPDES Permit Writers’ Manual for CAFOs

USDA-NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service). 1999.
National Engineering Handbook Part 651 Agricultural Waste Management Field Handbook.
U.S. Department of Agriculture, Washington, DC.
. A ccessed November 1, 2011.
USDA-NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service). 2003.
Conservation Practice Standards 313 (Waste Storage Facility) and 359 (Waste Treatment
Lagoon). U.S. Department of Agriculture, Washington, DC.
USDA-NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service). 2006.
Nutrient Management Conservation Practice Standard 590. U.S. Department of Agriculture,
Washington, DC.
USEPA (U.S. Environmental Protection Agency). N.d. Technical Fundamentals of Concentrated
Animals Feeding Operations (CAFOs) for Permit Writers and Inspectors. Session 1A
(Introduction/Overview of Livestock Agriculture), Slide 13. U.S. Environmental Protection
Agency, Washington, DC.

Endnotes
Portions of the information in this section are extracted or adapted from Harrison and Smith 2004a.

1

Portions of the information in this section are extracted or adapted from Fulhage 2000.

2

The typical content of a laboratory soil analysis report varies significantly from state to state. Typically, nitrogen,
phosphorus, and pH are reported. Micronutrients are rarely reported unless requested.

3

A list of consultants that are certified by NRCS to develop CNMPs in each state is available through USDA’s
Technical Service Providers (TSP) Registry (http://techreg.usda.gov/).

4

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NPDES Permit Writers’ Manual for CAFOs

Chapter

6

6. Protocols for Land Application of
Manure Nutrients
As explained in Chapter 4.1.7, any permit issued to a CAFO must include a requirement to imple­
ment an NMP that includes the BMPs necessary to meet the requirements of 40 CFR part 122.42(e)(1)
and for Large CAFOs the ELG of 40 CFR part 412. The relevant content in the NMP must be
integrated into the permit as enforceable terms of the permit. The terms of the NMP are the content
of the NMP that implements the regulatory requirements in part 122.42(e)(1). One of the nine
requirements in part 122.42(e)(1) are protocols for land application.1 Terms of the NMP relevant to
the protocols for land application must be incorporated as enforceable terms of any CAFO permit.
NMPs contain the technical information operations use to develop a plan that allows for maxi­
mum utilization of the nutrients in manure while minimizing the runoff of nutrients and
pollutants. The maximum utilization of
nutrients in manure depends on the amount
of manure that the operation will have, the
characteristics of that manure, the amount
of land the operation will have available,
and the type of crops and nutrient needs of
the crops that the operation plans to grow.
Although this chapter explains in more detail
the specific components of the NMP that are
the protocols for land application of manure,
40 CFR part 122.42(e)(1)(ix), it is important
for a permit writer to understand the source
of the information in the NMP itself and the
way it is used in the NMP to develop rates of
application and terms of the NMP.
Land application of manure slurry. (Photo courtesy of
USDA/NRCS)

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NPDES Permit Writers’ Manual for CAFOs

This chapter provides background information on soil fertility and plant availability of nutrients,
state technical standards for nutrient management, EPA’s regulatory requirements for land appli­
cation of manure, the permit term protocols for land application, and this chapter demonstrates
how to derive the permit terms for protocols for land application from a sample NMP.

6.1. Soil and Plant Availability of Nutrients
Soil is a pathway for nutrient flow to surface and ground water, and it is a medium for nutrient
transformations. Nutrient compounds are generally dynamic, undergoing various transforma­
tions depending on the properties of the soil they are in. Because those transformations affect
the amount and form of nitrogen and phosphorus available to the plant, appropriate manure and
fertilizer applications in an NMP will account for many of the transformations as discussed below.
Additionally, the CAFO rule requires accounting for some of those nutrient transformations
as permit terms. 40 CFR §§ 122.42(e)(5)(i)(A), (e)(5)(ii)(A). Therefore, it is important for a permit
writer to understand the behavior of nitrogen and phosphorus in the soil. For further supporting
information regarding soil science, see Appendix A, Basic Soil Science and Soil Fertility.

6.1.1. Nitrogen Cycle
Although nitrogen in soil is essential for plant growth, it is not always available in a form for
plant uptake. The largest pool of nitrogen is found in the atmosphere as an inert gas (N2). Plants
are not able to absorb gaseous nitrogen. Nitrogen must first have its form changed by biological
or industrial processes. The process that converts nitrogen gas into plant available forms of
nitrogen is called nitrogen fixation and is a part of the nitrogen cycle (Figure 6-1). In nature,
nitrogen becomes plant available when specialized bacteria (and to a lesser extent, lightning)
fix nitrogen gas. Leguminous plants, such as alfalfa and soybeans, have a symbiotic relationship
with nitrogen-fixing bacteria, in which the bacteria supply sufficient nitrogen to the plant and the
plant supplies carbohydrates to the bacteria. Because of that relationship, a legume crop is able to
supply its own nitrogen need and enrich a soil with nitrogen for crops that follow in the rotation
and therefore is considered an nitrogen credit.
The forms of nitrogen that plants typically use are ammonium (NH4+) and nitrate (NO3-).
Ammonium is used less by plants because it is extremely toxic in large concentrations.
Ammonium can oxidize in the soil to form nitrate through a two-step process that requires two
types of soil bacteria (Nitrosomonas and Nitrobacter). Nitrate is highly mobile and easily leached
as water moves through the soil profile, and can be a source of nitrogen pollution in surface and
ground water if it is not utilized by growing crops.
The majority of the nitrogen in the soil (95 to 99 percent) is locked up as organic compounds
(mostly as proteins) that are generally unavailable to plants. Organic nitrogen compounds become
plant available through a microbial process called mineralization. While mineralization converts
organic compounds into inorganic compounds, inorganic nitrogen can also be converted to
organic forms through a process called immobilization. Microbes require nitrogen, as all living
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients
6.1.1. Nitrogen Cycle

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-3

NPDES Permit Writers’ Manual for CAFOs

Figure 6-1. The Nitrogen Cycle.

organisms do, for basic cellular function. Nitrogen is required for microbial decomposition
of organic residues. Microbes use available inorganic nitrogen from the soil, which becomes
incorporated into their microbial cellular structure. That nitrogen is unavailable until the
organisms die and decompose, releasing plant available inorganic nitrogen back to the soil.
Nitrogen compounds can also be released to the atmosphere as ammonia gas (NH3) through
a process called volatilization. Warm, moist soils and surface application of manure and
wastewater accelerates volatilization. While ammonia can be lost to the atmosphere, it can also
be removed from the atmosphere via absorption through plants. The other significant pathway for
gaseous loss of nitrogen is denitrification. Denitrification is a series of bacteria-driven reduction
reactions that reduce nitrate ultimately to nitrogen gas. Because denitrification is a reduction
reaction, it requires an anaerobic environment, such as saturated soils. Only when soil oxygen
levels are low enough will nitrate be fully reduced resulting in the formation of nitrogen gas.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients
6.1.1. Nitrogen Cycle

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

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NPDES Permit Writers’ Manual for CAFOs

6.1.2. Phosphorus Cycle
Phosphorus in soil mostly comes from weathered apatite rock. Other sources of soil phosphorus
include decomposing organic matter and humus. Plant available forms of phosphorus include
hydrogen phosphate (HPO4-2) and dihydrogen phosphate (H2PO4-). Phosphorus’s tendency to
bond with other compounds and with the clay fraction in the soil can reduce the mobility of the
nutrient. Soil pH also has a strong influence on the availability of phosphorus. The phosphorus
cycle is shown in Figure 6-2.
Both the inorganic and organic phosphorus forms are distributed among three major soil pools:
solution phosphorus, active phosphorus, and fixed phosphorus. The solution pool contains
dissolved, soluble phosphorus that is readily available for plant uptake. While that pool is
generally small, relative to the total amount of phosphorus, it is important because it is the only
pool from which plants can draw nutrients. Because plants are continuously removing nutrients
from this pool, it must be replenished.

Figure 6-2. The Phosphorus Cycle.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients
6.1.2. Phosphorus Cycle

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-5

NPDES Permit Writers’ Manual for CAFOs

The active pool is capable of replenishing the solution pool. The active pool contains phosphorus
that is somewhat less available than the solution pool. This pool contains phosphorus in several
different forms:
▶ Phosphorus that is loosely adsorbed to mineral surfaces, on active mineral sites.
▶ Phosphorus that has reacted with other elements to form somewhat insoluble
compounds.
▶ Organic phosphorus that is easily mineralized.
While the active pool does not contain soluble phosphorus, the
active pool can easily release phosphorus to the solution pool.
The relationship between the solution and active pools can be
described by the cycle shown in Figure 6-3. As phosphorus is
added to the solution pool, more phosphorus is adsorbed to
mineral surfaces and as the solution pool is depleted, the active
pool will release additional phosphorus to replenish it.
Some exchange occurs between the solution and active pools.
When phosphorus is initially added to a soil, it can first be
held in complexes of low solubility or by temporary bonds,
as part of the active pool, that can be released back to the
solution pool and be made plant available. However, with
time, the compounds will become more and more insoluble
and contribute to the third pool—fixed phosphorus. Fixed
phosphorus is extremely insoluble and can remain there
for many years without becoming available to a plant and
contributing minimally to a soil’s fertility.

Figure 6-3. The relationship between the
phosphorus solution and the active pool.

Soils have a phosphorus fixation capacity that is defined by the sites on a mineral surface that
are available to react with phosphorus. Historically, there has been very little plant available
phosphorus in many soils because of that fixation capacity. If enough soluble phosphorus is
added to a soil, the reactive sites become occupied so that any further phosphorus that is applied
will remain in the solution pool. Soils that have been regularly over-applied with phosphorus
might have relatively high levels of soluble phosphorus because the soil’s capacity to fix
phosphorus has been overwhelmed. In those cases, dissolved phosphorus can be leached from
soils and lost to groundwater through the soil profile or to surface water in runoff.
Regardless of the potential for dissolved phosphorus leaching or runoff, there is always a potential
for losses of phosphorus to surface waters from erosion. Because phosphorus binds to soil particles,
if soil particles are eroded from a landscape, the attached phosphorus (and any other nutrients,
metals, or contaminants) are lost as well. Phosphorus can be released from the soil particle it is
bound to if the chemical bond holding it together is broken. For example, the oxidized form of iron
forms a strong bond with phosphorus. However, if iron is reduced, the bond will break and release
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients
6.1.2. Phosphorus Cycle

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-6

NPDES Permit Writers’ Manual for CAFOs

phosphorus. When phosphorus is bound to soil sediments by iron and the soil is eroded to surface
waters such as an anaerobic lake or pond, iron will be reduced and release iron-bound phosphorus
from the soil particle to the waterbody. Agricultural management practices must consider the
potential for this type of phosphorus loss. 40 CFR §§ 122.42(e)(1)(vi), 412.4(c)(2)(i).
Many factors must be considered when applying phosphate fertilizer, including soil fertility
levels, crops to be grown, tillage methods, equipment, timing, slope, climate, and other
management factors so that both dissolved and particulate phosphorus are adequately controlled
while supplying the necessary crop nutrient requirements.

6.1.3. Soil Fertility
Soil fertility is the ability of a soil to provide nutrients for plant growth. Although soils contain
most of the nutritional elements plants require, only a small percentage is available for plant
up­take. Plants generally derive nitrogen, phosphorus, potassium, calcium, magnesium, and
sulfur from soil. Many factors affect the availability of nutrients in soil, including the forms of the
nutrient in the soil, pH, soil aeration, soil compaction, soil temperature, and soil moisture. The
essential nutrients for plant growth move through the soil profile at various rates, depending on
their chemical properties. An understanding of the chemical properties of those elements and the
amounts available to plants is necessary when determining the amount of fertilizer or manure to
be added to a soil to prevent over application, which in time could result in surface and ground
water contamination.
The ability of a soil to retain nutrients is related to its cation exchange capacity (CEC). CEC is a
measure of the soil’s ability to retain cations (positively charged ions) and is indicative of the
soil’s fertility. Soil minerals have a net surface charge, which is usually negative, that allows them
to hold and retain cations against leaching. The net negative charge of a soil is largely attributed to
the clay and organic matter contained in the soil. Negatively charged soil particles will naturally
attract positively charged ions and repel negatively
charged ions. That explains why positively charged
nutrients such as ammonium, will remain adsorbed
to clay particles in the soil, while negatively charged
nutrients such as nitrate are easily leached out
of the soil. The CEC of a soil directly affects the
soil’s nutrient storage capacity and, therefore, the
amount of fertilizer or manure that should be used
and the frequency with which fertilizer or manure
should be applied.

Water runoff eroding a field. (Photo courtesy of
USDA/MO NRCS)

The movement of nutrients in soil is largely con­
trolled by the movement of water through and over
a soil. Two pathways are (1) the infiltration and
percolation or drainage of water through the soil
profile; and (2) runoff water over the soil surface.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients
6.1.3. Soil Fertility

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-7

NPDES Permit Writers’ Manual for CAFOs

Percolation results in the loss of soluble compounds (leaching), thus depleting soils of needed
plant nutrients. Runoff losses generally include water, appreciable amounts of soil (erosion) and
any nutrients, chemicals, or compounds that are attached to the displaced soil particles.

6.2. Using Manure Nutrients
Manure is land applied because it contains nutrients (i.e., nitrogen, phosphorus and potassium)
and acts as a fertilizer by supplying crop nutrient needs; it also contains organic matter, which
improves the quality of the soil by decreasing compaction, increasing water-holding capacity,
and, increasing the CEC, among other benefits. Typically, manure is applied so that it supplies
either the nitrogen or phosphorus requirements of the crop to which it is applied. Manure is
typically excreted at an nitrogen to phosphorus ratio of 2 or 3 to 1, while the typical crop’s nutrient
need of nitrogen and phosphorus is in a ratio ranging from 4 to 9 pounds of nitrogen per pound
of phosphorus. That means that up to 3 times the needed amount of phosphorus is applied when
manure is applied to meet the nitrogen requirements (disregarding nutrient losses). Table 6-1
shows typical nutrient concentrations for various types of manure. Table 6-2 shows typical
nutrient requirements for some common crops. The values shown in these tables are generalized
and might not be typical of all locations. When developing an NMP, site-specific values should
be used where available. State-specific book values should be used where site-specific data are
not available. Because of the 2 or 3 to 1 nitrogen to phosphorus ratio of manure, meeting nitrogen
requirements through manure application alone can lead to a buildup of phosphorus in the soil
and correspondingly high or very high soil test phosphorus levels.

Land application of dairy waste via “big gun” effluent distribution system.
(Photo courtesy of USDA/NRCS)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-8

NPDES Permit Writers’ Manual for CAFOs

Table 6-1. Manure nutrient content factors
Manure nutrient content (pounds per ton of manure)
Nitrogen
Animal type
Beef cows
Milk cows
Heifer and heifer calves
Steers, calves, bulls, and bull calves
Breeding hog and pig

As excreted
10.95
10.69
6.06
10.98
13.26

Phosphorus*

After losses
3.30
4.30
1.82
3.30
3.32

As excreted
3.79
1.92
1.30
3.37
4.28

After losses
3.23
1.65
1.10
2.86
3.62

3.29

2.80

Other hog and pig

11.30

2.82

Hens and pullets of laying age

26.93

18.64

9.98

8.50

Pullets over 3 months but not laying
Pullets under months
Broilers
Turkeys for slaughter

27.20
27.20
26.83
30.36

13.60
13.60
16.10
16.18

10.53
10.53
7.80
11.83

8.95
8.95
6.61
10.06

Turkeys for breeding

22.41

11.20

13.21

11.23

* Phosphorus presented here is elemental phosphorus. To convert to the orthophosphate (P2O5) form, multiply the
elemental phosphorus by 2.29.

Table 6-2. Nutrient uptake parameters for selected crops used to estimate the assimilative
capacity of cropland. These values are for the harvested portion of the crop that is removed from the field at harvest.

Crop

Yield unit

Field corn, for grain

Bushel

Field corn, for silage

Ton

Pounds per
yield unit

Nutrient content - pounds
per yield unit
Nitrogen

Phosphorus

56

0.80

0.15

2,000

7.09

1.05

Oats

Bushel

32

0.59

0.11

Barley

Bushel

48

0.90

0.18

Soybeans

Bushel

60

3.55

0.36

Alfalfa hay

Ton

2,000

50.40

4.72

Bermuda grass seed
Winter wheat harvested (soft)
Winter wheat harvested (hard)
Canola
Rice

Pound
Bushel
Bushel
Pound
Bag

1
60
60
1
100

0.040
1.02
1.23
0.035
1.25

0.005
0.20
0.23
0.006
0.29

Rice for grain

Bushel

56

1.07

0.18

Sorghum hay

Ton

2,000

2.39

1.01

Sugar beets for seed

Pound

1

0.024

0.020

Sugar beets for sugar (w/o crown)
Triticale
Wild rice

Ton
Bushel
Pound

2,000
56
1

4.76
1.50
0.013

0.94
0.17
0.003

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-9

NPDES Permit Writers’ Manual for CAFOs

In some areas, animal waste application rates might
need to be based on parameters other than nitrogen or
phosphorus. For example, trace metals present in animal
wastes, when applied at either nitrogen- or phosphorusbased rates, provide many of the micronutrients necessary
for plant growth. Excessively high levels of the trace metals,
however, can inhibit plant growth. By limiting manure
applications to the nitrogen- and phosphorus-based rate,
CAFOs will also be limiting the rate at which metals are
applied to fields and thus reduce the potential for applying
excessive amounts of the trace metals. In other regions
of the country where farmlands are overloaded with
salt, the salt content of animal waste, often measured as
electrical conductivity, might be the appropriate parameter
for limiting land application rates. When using any of
those alternative application rates, CAFOs must ensure
appropriate agricultural use of the nutrients in the manure.
In no case may manure be applied at rates greater than the
annual nitrogen needs of the crop(s).
NRCS staff and landowner use the soil probe to

The animal agricultural industry has seen the
take a soil sample on farm.
(Photo courtesy of USDA/NRCS)
consolidation of many smaller operations into a smaller
number of larger operations (Kellogg et al. 2000). Many
livestock and poultry producers do not have adequate
land to utilize the manure nutrients generated on-site in a manner that does not exceed crops
needs. Figures 6-4 and 6-5 illustrate that in some counties, the production of recoverable manure
nutrients exceeds the assimilative capacity of all the cropland and pastureland available for
manure application in that county.
Consolidation in the animal agriculture industry has created regional surpluses of phosphorus
and a buildup of soil phosphorus levels, as indicated by Figure 6-6. Phosphorus buildup is
one variable that can contribute to phosphorus loss. However, other factors can result in high
phosphorus loss even when the soil test phosphorus is low. Unfortunately, problems associated
with high soil phosphorus levels are aggravated by the fact that many of these agricultural
soils are in states with sensitive waterbodies, such as the Great Lakes, Lake Champlain, the
Chesapeake Bay and Delaware Bay, Lake Okeechobee, and the Everglades.
The overall goal of efforts to reduce phosphorus loss to water should be to balance phosphorus
inputs and outputs at the farm and watershed levels while managing soil and phosphorus in
ways that maintain productivity. Management strategies that minimize phosphorus loss to water
can involve one or more of the following approaches: optimizing phosphorus use efficiency,
refining animal feed rations, using feed additives to increase animal absorption of phosphorus,
transporting manure from surplus areas to deficit areas, increasing the number of acres available

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-10

NPDES Permit Writers’ Manual for CAFOs

Figure 6-4. Excess manure nitrogen.

Figure 6-5. Excess manure phosphorus.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-11

NPDES Permit Writers’ Manual for CAFOs

to an operation for land application, and
applying conservation practices like reduced
tillage, buffer strips, and cover crops in
critical areas of phosphorus export from a
watershed.
Because of the potential for phosphorus
buildup where manure utilization plans are
based on nitrogen, soils in fields receiving
livestock manure should be tested regularly
with close monitoring of phosphorus levels
as well as the risk for phosphorus transport
from the field.

6.3. Standards for
Nutrient Management

Figure 6-6. Percent of soils testing medium or low in phosphorus.
(Source: USDA/NRCS)

Utilizing manure nutrients can be a beneficial practice that improves the health of the soil and
replaces the use of purchased commercial fertilizer. However, that requires proper management
of the amount, form, source, timing, and placement of the nutrients. Various standards exist for
the management of nutrients. USDA-NRCS develops national conservation practice standards for
nutrient management. Each state’s NRCS office adopts and may modify those practices that are
applicable in that state. Some state NRCS offices also develop state-specific standards that are not
found in the national handbook. For standards to which NPDES permit writers and inspectors
can refer, see Appendix K, NRCS Conservation Practice Standards. NRCS Conservation Practice
Standard Code 590,2 Nutrient Management, is intended to guide the proper land application of
nutrients. The standard states that nutrient application rates are to be established that consider
current soil tests, realistic yield goals and management capabilities. In cases where manure is the
source of applied nutrients, the rate also must be based on an analysis of the nutrient content of
the manure, NRCS book values, or historical documented records.
NRCS conservation practice standards often
rely on guidelines established by the state’s land
grant university. Land grant universities establish
guidelines for many procedures involved with
nutrient management. Some examples can include
▶ Crop yield goals.
▶ Fertilizer recommendations.
▶ Manure excretion rates.
▶ Field risk assessment tools for nitrogen,
phosphorus, and erosion.
Chicken litter spreading. (Photo courtesy of USDA/NRCS)

▶ How to calibrate equipment.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-12

NPDES Permit Writers’ Manual for CAFOs

▶ Nutrient use efficiency strategies.
▶ Emerging technologies.
Private industries also develop some of their own standards. For instance, many private soil
and manure testing labs develop their own nutrient recommendations on the basis of soil test
analyses. Those private standards might or might not be recognized by the land grant university
in a state.

6.3.1. EPA’s State Requirements for Land Application
The CAFO regulations require states to establish technical standards for nutrient
management that are consistent with 40 CFR part 412.4(c)(2). 40 CFR § 123.36. The regulation
at 40 CFR part 412.4(c)(2) requires that those technical standards include a field-specific
assessment of the potential for nitrogen and phosphorus transport from the field to waters of
the U.S. In addition, the standards must address the form, source, amount, timing, and method
of application of nutrients on each field to achieve realistic production goals while minimizing
nitrogen and phosphorus movement to waters of the U.S. Id.

40 CFR § 412.4(c)(2)
Best Management Practices (BMPs) for Land Application of Manure, Litter, and
Process Wastewater
Determination of application rates
Application rates for manure, litter, and other process wastewater applied to land under the owner­
ship or operational control of the CAFO must minimize phosphorus and nitrogen transport from
the field to surface waters in compliance with the technical standards for nutrient management
established by the Director. Such technical standards for nutrient management shall:
(i) Include a field­specific assessment of the potential for nitrogen and phosphorus transport
from the field to surface waters, and address the form, source, amount, timing, and
method of application of nutrients on each field to achieve realistic production goals, while
minimizing nitrogen and phosphorus movement to surface waters; and
(ii) Include appropriate flexibilities for any CAFO to implement nutrient management practices
to comply with the technical standards, including consideration of multi-year phosphorus
application on fields that do not have a high potential for phosphorus runoff to surface water,
phased implementation of phosphorus­based nutrient management, and other components,
as determined appropriate by the Director.

Requirements for State Technical Standards
All technical standards must identify an appropriate field-specific assessment method for
determining nutrient transport to be used when developing rates for land application. Technical
standards for nutrient management also establish methods and criteria for determining
application rates that must appropriately balance the nutrient needs of crops and potential adverse
water quality impacts, in accordance with the risk of nutrient transport. 40 CFR § 412.4(c)(1). To
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.3.1. EPA’s State Requirements for Land Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-13

NPDES Permit Writers’ Manual for CAFOs

achieve that objective, technical standards must address the source, amount, timing and method
of application for each form of manure nutrients. 40 CFR § 412.4(c)(2)(i).

Nutrient Transport Risk Assessment
The field-specific assessment provides CAFOs with the information needed to determine whether
manure nutrients should be applied at an nitrogen- or phosphorus-based rate, or if manure
application is not appropriate. CAFOs may apply a combination of conservation practices, BMPs,
and management activities, which in aggregate can reduce a field’s vulnerability of phosphorus
transport to waters of the U.S. Regardless of what assessment method is required by a state,
it must at least include an analysis of soil phosphorus. 40 CFR §§ 122.42(e)(5), 412.4(c)(3). As
discussed in Chapter 5, sample handling can affect soil test results and extraction procedures
used for different analysis are typically tailored to a region. Therefore, technical standards need
to also address how soil samples are to be collected, the extraction procedures, methods or
laboratories that are to be used for analyzing different nutrients and the frequency with which the
analyses should occur.

Form and Source
The form and source of the manure must be
identified for all manure that is planned for land
application. 40 CFR § 412.4(c)(2)(i). The term
form of manure may be identified as solid, liquid,
semi-solid, or slurry. The term source refers
to the specific storage structure or location at
which manure is held until it is land applied. The
manure’s form will directly determine the type of
storage needed. Liquid and semi-solid or slurry
manures are typically stored in a type of lagoon
or holding pond. Solid manures are typically
stored in sheds or stockpiles, which can be on a
concrete pad or other impervious material. For
further discussion of manure types and storage,
see Chapter 4 of EPA’s development document for
the 2003 CAFO rule revisions (EPA‑821-R-03-001)
(USEPA 2003).

Turkey litter stockpile. (Photo courtesy of USDA/NRCS)

Amount
Because the amount of manure to be applied relies on the amount of nutrients in the manure,
technical standards need to ensure that manure nutrient analyses represent the manure that is
applied. Similar to soil testing, the handling of a sample can affect the outcome of the test results.
For example, some manure nitrogen is lost through volatilization during the handling and storage
of the manure. The manure nutrient analysis accounts for volatilization losses that have occurred
up to the time at which the samples for the analysis are taken. Therefore, technical standards
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.3.1. EPA’s State Requirements for Land Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-14

NPDES Permit Writers’ Manual for CAFOs

need to address appropriate sampling methods and acceptable methods or laboratories that
should be used for performing the analyses to ensure the results represent the nutrient content of
the material that will be applied to a field.
A separate manure analysis needs to be provided for each form (e.g., stockpiled solids, separated
solids, lagoon or pond liquid, lagoon or pond sludge) of animal manure stored on-site where the
manure nutrient content is expected to vary to have test results that accurately reflect the nutri­
ents in the manure that is land applied. See 40 CFR parts 412.4(c)(1) and (c)(3). Not only will the
composition of the forms be different, they often are applied to the land separately from each
other. For example, liquids from a holding pond could be irrigated weekly to a field, whereas the
solids might be land applied just once or twice per year to remotely located fields. There could
be circumstances where sampling of every single source might be less important. For example it
could be reasonable to expect a dairy with multiple barns that are each designed, operated, and
managed under the same set of variables would generate manure with similar nutrient content.
When each barn houses the same number of cows, the cows are fed the same diet and are on the
same milking schedule, and each barn is designed to handle and store manure in the same man­
ner (e.g., freestall barns with push pits at the end of each barn), sampling of both pits is probably
not necessary. For more information on manure testing protocols, see Chapter 5.9.
The amount of nutrients to be applied, from both organic and inorganic sources also depends on
the realistic production goals, and the nutrient needs for a given crop to meet the realistic yield
goal. The criteria for deriving realistic yield goals including criteria for adjusting yield goals on
the basis of actual crop yields should be provided by the technical standard as that will affect
the amount of nitrogen and phosphorus that will be applied to the land. It might be insufficient
for the technical standard to simply require development of realistic yield goals; the specific
basis(es) for the yield goals should be described. Unrealistic yield goals will result in an overapplication of nutrients.
Residual plant available nitrogen (PAN) in the soil affects the amount of additional nutrients
that should be applied to meet crop nitrogen needs. Because organic forms of nitrogen typically
become plant available when they are converted to inorganic forms, such as nitrate and
ammonium, crediting generally identifies the amount of organic nitrogen likely to be converted
to inorganic forms that will be plant available. Crediting for all residual nitrogen in the field
that will be plant available, as a result of prior additions, should be done in accordance with the
directions provided in the technical standards. That will include appropriate mineralization rates
to be used in determining the amount of available nitrogen that has slowly become available from
previous manure applications and the amount of PAN from a prior legume crop.
The amount of available nutrients will also fluctuate with the method of land application
(e.g., spray irrigation, surface application, with or without incorporation). The method of land
application will affect the amount of nitrogen that will volatilize, thus affecting the amount of
manure that needs to be applied to meet realistic yield goals. Therefore, volatilization rates to be
applied to various application methods should be provided by the technical standards.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.3.1. EPA’s State Requirements for Land Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-15

NPDES Permit Writers’ Manual for CAFOs

Timing
Under certain circumstances, usually
related to seasonal conditions, CAFO land
application areas might be more likely to
generate runoff that reaches waters of the
U.S. Accordingly, technical standards must
address timing considerations as to when
land application should be delayed and/or
prohibited to minimize nutrient movement
to surface waters. 40 CFR § 412.4(c)(2)(i). To
minimize movement of nutrients to waters
of the U.S., technical standards for nutrient
management should prohibit application of
Heavy frost on a stream buffer. (Photo courtesy of USDA/NRCS)
manure and process wastewater to saturated
ground where appropriate. The technical
standards should prohibit surface application of manure and process wastewater during rainfall
and when rainfall is expected soon after a planned application, if the rainfall might produce
runoff and the runoff might enter waters of the U.S. The standards should either prohibit
application of manure and process wastewater on snow, ice, and frozen ground, or include
specific protocols that CAFO owners or operators, nutrient management planners, and inspectors
will use to conclude whether application to a frozen or snow- or ice-covered field (or a portion
thereof) poses a reasonable risk of runoff. Where there is a reasonable risk, the standards should
prohibit application to the field or relevant portion thereof during times when the risk exists or
could arise. Manure storage structures need to include adequate capacity to store material that
accumulates during those times when, under the technical standards for nutrient management,
land application would be prohibited. 40 CFR § 122.42(e)(1)(i).
For example, in Michigan, the technical standard for nutrient management includes an explicit
prohibition of manure application under certain conditions :
1. CAFO waste shall not be applied on land that is flooded or saturated with water at the
time of land application.
2. CAFO waste shall not be applied during rainfall events.
3. CAFO waste shall not be surface applied without incorporation to frozen or snowcovered ground, except in accordance with the Department 2005 Technical Standard
for the Surface Application of CAFO Waste on Frozen or Snow-Covered Ground without
Incorporation or Injection.
4. CAFO waste application shall be delayed if rainfall exceeding one-half inch, or less if a
lesser rainfall event is capable of producing an unauthorized discharge, is forecasted by
the National Weather Service (NWS) during the planned time of application and within
24 hours after the time of the planned application. Forecast models to be used are at
http://www.weather.gov/mdl/synop/products.php.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.3.1. EPA’s State Requirements for Land Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

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NPDES Permit Writers’ Manual for CAFOs

The ELG does not establish national requirements prohibiting manure application to frozen,
snow-covered, or saturated ground, or before forecasted rain. Runoff associated with such
application could depend on a number of site-specific variables, including soil type, topographic
variability (i.e., slope of the land), and distance to waters of the U.S. States are better able to
tailor their technical standards to reflect the site-specific conditions that warrant prohibitions
or limitations on manure applications to frozen, snow-covered, or saturated ground, or before
forecasted rain. In general, EPA strongly encourages states to prohibit application to frozen, snowcovered, or saturated ground, and when the forecast calls for rain in an amount that is likely to
produce runoff because crops are unable to utilize the nutrients during such conditions and,
therefore, typically results in runoff of nutrients. For additional guidance on addressing winter
spreading, see Appendix G, Winter Spreading Technical Guidance and Appendix E, Minimum
Depth of Rain at Which Runoff Begins.
If technical standards for nutrient management do not prohibit manure application on frozen,
saturated, or snow covered ground, the protocols for land application under those circumstances
should account for the form of the manure to be applied (e.g., liquid, semi-solid, or dry manure),
the time at which the manure would be applied relative to periods when runoff may occur, the
fraction of precipitation that runs off the land in melt water and in response to winter rains (as
affected, in part, by whether soil is frozen), the time it takes runoff to travel to waters of the U.S. (as
affected by the slope of the land, distance to waters, roughness of the land surface, and whether
runoff is in contact with land surface), and other relevant factors, as appropriate.

Flexibility to Implement Nutrient Management Practices
Technical standards for nutrient management can allow certain flexibilities for implementing
nutrient management practices. 40 CFR § 412.4(c)(2)(i). The CAFO regulations specifically allow
for the consideration of multi-year phosphorus application on fields that do not have a high
risk for phosphorus runoff to waters of the U.S. Id. Multi-year phosphorus application is an
approach that allows a single application of manure phosphorus to be applied at a rate equal
to the recommended phosphorus application rate or phosphorus removal in harvested plant
biomass for the crop rotation for multiple years in the crop sequence. However, under any multiyear phosphorus application, the rate at which manure nutrients are applied cannot exceed the
annual nitrogen recommendation of the year of application. 68 FR 7,210 (Feb. 12, 2003). The field
must also not receive additional phosphorus until the amount applied in the single year has been
removed through plant uptake and harvest. 40 CFR § 412.4(b)(3).

Additional Standards
While the state’s technical standards need to be detailed in addressing the form, source, amount,
timing and method of application for the use of each form of manure nutrients, they may also
contain additional requirements that the state chooses to address. Those could include specific
requirements that address animal feed management, additional soil testing (i.e., nitrogen testing
requirements), implementing specific BMPs (i.e., cover crops), or any other practices the state

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.3.1. EPA’s State Requirements for Land Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-17

NPDES Permit Writers’ Manual for CAFOs

deems necessary to minimize nitrogen and phosphorus transport to surface waters. Additional
considerations necessary for protecting surface waters are left to the discretion of the state
Director when establishing technical standards. 68 FR 7,198 (Feb. 12, 2003).

6.4. EPA’s CAFO Requirements for Land Application
Any permit issued to a CAFO must include the requirement to implement a nutrient manage­
ment plan that includes protocols for land application. 40 CFR § 122.42(e)(1). As discussed in
Chapter 4.1.3 of this Manual, permitted Large CAFOs subject to ELG subparts C and D must land
apply manure nutrients in accordance with certain practices defined by the ELG. 40 CFR § 412.4.
Those include following the state’s technical standards for nutrient management3 as discussed in
Section 6.3.1. Id.; at § 4(c). Briefly the ELG require the following:
▶ A field-specific assessment of the potential for nitrogen and phosphorus transport
from each field where manure is to be applied and using the results in developing
application rates. 40 CFR § 412.4(c)(2)(i).
▶ Land application of manure, litter, and process wastewater at application rates
that minimize phosphorus and nitrogen transport from the field to waters of
the U.S. in compliance with the technical standards for nutrient management.
40 CFR § 412.4(c)(2).
▶ Consideration of the manure and soil analyses in the development of the application
rates. 40 CFR § 412.4(c)(3).
▶ Inspections of equipment used for land application. 40 CFR § 412.4(c)(4).
▶ Development of appropriate setbacks
and buffers. 40 CFR § 412.4(c)(5).
▶ Documentation of appropriate
BMPs as well as other necessary
record keeping requirements.
40 CFR § 412.37(c).
As discussed throughout this chapter,
numerous variables, including those listed
above, are considered when developing
appropriate land application rates for manure,
litter and process wastewater. Technical
standards, as discussed above, form the
foundation for determining the appropriate
rates of application.

A nutrient management planner reviews field conditions and
implementation of BMPs to conduct a field risk assessment
and calculate appropriate land application rates.
(Photo courtesy of USDA/NRCS)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-18

NPDES Permit Writers’ Manual for CAFOs

A Note on the Orientation of Chapter 6:
Section 6.5 of this chapter provides an in-depth discussion of protocols for land application and
discusses how a permit writer can derive permit terms for protocols for land application from an
NMP, as required in 40 CFR part 122.42(e)(1). As discussed in Chapter 4.1.7, a permit writer may
identify the protocols for land application as a permit term by using one of three methods. Section
6.6 illustrates how a permit writer can derive terms for protocols for land application from an NMP,
using the third method discussed in Chapter 4, which specifically describes each term of the NMP
in detail. A permit writer taking that approach would extract from the NMP all the relevant values
for all the components that together encompass the term protocols for land application.

6.5. Protocols for Land Application
The CAFO regulations require site-specific terms of an NMP to be included in a CAFO’s NPDES
permit. Technical standards form the basis for critical elements of the site-specific terms of the
NMP because they are the foundation from which an NMP is developed. EPA has clarified what a
technical standard should include to adequately meet the requirements of 40 CFR part 412.4(c)(2)
when used to develop an NMP that contains all the required terms of the NMP (See Appendix I,
NPDES CAFO Technical Standard Review Checklist).
Land application rates in NMPs are uniquely developed
for each field and must be included in the permit as site
specific permit terms. 40 CFR § 122.42(e)(5). Fields and
field-specific rates of application of manure cannot be
captured with broadly applicable permit conditions. (For
an introduction of the concepts of broadly applicable
versus site-specific terms, see Section 4.1.7.) The remainder
of this chapter discusses and provides example permit
terms that should be used as guidance for understanding
what in the NMP should be identified as a permit term
under both the linear and narrative rate approach.

Land application of manure using lay-flat hose
system. (Photo courtesy of USDA/NRCS)

With respect to rates of application, a CAFO permit must
be written to express the terms of the NMP for protocols for
land application using either the linear or narrative rate
approach. 40 CFR § 122.42(e)(5). Many NMPs are developed
such that the permit terms may be written to meet either
the linear or narrative rate approach. In essence, both
approaches require the same information. However, the
linear and narrative rate approaches differ in the way the
site-specific land application rates and the information used
to develop them are expressed in the NMP and incorporated
as terms of the permit. Under the linear approach, certain
required information is captured as permit terms, while

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

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NPDES Permit Writers’ Manual for CAFOs

under the narrative rate, much of the same
information is captured as part of a complex
term, identified in the CAFO regulations as the
methodology. Under the linear approach, the
NMP as submitted with the NOI is the NMP
that is to be implemented over the 5 years of
permit coverage. The rates, methods, timing,
and source of manure nutrients (among other
items) are to be applied as predicted by the
NMP. The linear approach is for operators
who do not anticipate that the NMP will
change once it is developed. The narrative rate
approach allows the NMP the flexibility for
some changes to occur as it is implemented
Cover crop BMPs can reduce the risk of phosphorus transport
over 5 years of permit coverage. The source of
by minimizing soil erosion. (Photo courtesy of USDA/NRCS)
manure and the rates, methods, and timing of
application are some of the elements that may
change over the life of the permit without requiring changes to the terms of the NMP.
For each approach, the CAFO rule identifies the required, minimum terms of the NMP specific
to that approach. The linear approach expresses field-specific maximum application rates in
terms of the amount (in pounds) of nitrogen and phosphorus from manure allowed to be applied.
40 CFR § 122.42(e)(5)(i). The narrative rate approach expresses the field-specific application rates
by identifying the way in which the site-specific NMP determines how to calculate the amount
of manure allowed to be applied while including limits on the maximum amounts of nitrogen
and phosphorus derived from all sources of nutrients. Id at (e)(5)(ii). Under either approach, the
projected amount of manure to be land applied is not a permit term because it depends on the
concentration of nutrients in the manure. However, specifying the actual amount of manure
applied must be reported in the annual report. Id. Under both approaches, the amount of
manure to be land applied is a projected amount that must be recalculated at least once a year.
40 CFR §§ 122.42(e)(5)(i)(B), (5)(ii)(D).
There is more than one way for the permit writer to adequately express the terms of the NMP
as permit requirements, particularly given the flexibilities provided by the narrative rate
approach. As discussed, state-specific requirements for nutrient management vary from one
state to another. Field risk assessment tools differ in the site characteristics they include and
the frequency with which they are run. Some states’ risk assessment tools factor in current and
previous manure applications while others do not. Some states require nitrogen soil testing in
addition to phosphorus soil testing, and soil testing frequency can range from 1 to 5 years. Those
types of variation affect how agronomic rates are developed in an NMP. Section 6.5 provides one
approach for writing narrative rate permit term requirements. Permit writers need to understand
their state’s regulatory requirements and technical standards for nutrient management, as well as
the minimum requirements of the linear and narrative rate approaches, so they can develop sitespecific permit terms that meet the requirements of their state-specific CAFO programs.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-20

NPDES Permit Writers’ Manual for CAFOs

6.5.1. Site-Specific Terms: Linear and Narrative Rate
Approaches
Table 6-3 outlines the terms associated with protocols for land application for each approach. As
shown in Table 6-3, six site-specific terms apply to both the linear and narrative rate approaches
for expressing land application rates in NMPs. 40 CFR §§ 122.42(e)(5)(i)(A), 122.42(e)(5)(ii)(A). Six
additional permit terms apply when using the linear approach. 40 CFR § 122.42(e)(5(i)(A). Those
additional linear approach permit terms address site-specific information that is also addressed
under the narrative rate approach. The difference is that, in the narrative rate approach, the linear
approach permit terms are factors of the methodology, rather than terms of the NMP. The factors
are not themselves required to be terms in the narrative rate approach, but the methodology
used to account for them in the CAFO’s NMP is a term. Under the narrative rate approach, the
methodology is the enforceable permit term, rather than the factors that it must encompass.
Sections 6.5.1, as follows, 6.5.2, and 6.5.3 discuss in depth the elements listed in Table 6-3 and the
important role each plays in the NMP, regardless of whether they are captured under the linear or
narrative rate approach.
Table 6-3. Field-specific land application protocol terms
Term
Term
linear
narrative
approach
rate

NMP Components
Fields available for land application

X

X

Timing limitations for land application

X

X

Outcome of the field-specific assessment of the potential for nitrogen and
phosphorus transport from each field

X

X

Planned crops or other use

X

X

Realistic annual crop yield goal

X

X

Total nitrogen and phosphorus recommendations per crop

X

X

Credits for plant available nitrogen

X

Consideration of multi-year phosphorus application

X

Accounting for all other additions of plant available nitrogen and
phosphorus to the field

X

Method and timing of land application

X

Form and source of manure, litter, and process wastewater

X

Maximum pounds of nitrogen and phosphorus from manure, litter, and
process wastewater

X

Methodology to account for the amount of nitrogen and phosphorus in
the manure to be applied

X

Maximum amount of nitrogen and phosphorus from all sources

X

Alternative crops

X

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

Table 6-3. Site-specific and field-specific land application protocol terms (continued)
Term
Term
linear
narrative
approach
rate

NMP Components
Methodology to account for
• Soil test results
• Credits for plant available nitrogen in the field
• The amount of nitrogen and phosphorus in the manure, litter, and
process wastewater to be applied
• Consideration of multi-year phosphorus application
• Accounting for all other additions of plant available nitrogen and
phosphorus to the field
• Form and source of manure, litter, and process wastewater
• Timing and method of land application
• Volatilization of nitrogen and mineralization of organic nitrogen

X

Fields Available for Land Application
The NMP must identify each field where land application will occur. The CAFO
regulations require each field included in the NMP to be a site-specific term of the permit.
40 CFR § 122.42(e)(5). Each field should have a unique name or code and include the number of
acres making up the field. Field maps that are appropriately labeled should also be included in the
NMP. The labels from the field maps should be easily matched to all fields listed through the NMP.
Otherwise, it might be difficult to correlate other terms associated with each field, thus making it
difficult for the permit writer to correctly establish the terms of the NMP.
Technical standards may limit the allowable
size of a field by setting limits on the acres that
a soil sample can represent. Many standards
set limits ranging from 10 to 30 acres. For
example, if the soil sample shows that a 30acre portion of a 100-acre field has significantly
different soil nutrient content than the rest
of the field, that 30-acre portion should be
managed separately to meet the objective of
nutrient management planning. Conversely,
many standards allow fields with similar
allowable application rates to be combined.
For example, Missouri’s technical standard
requires the average field area represented by
a soil sample to be approximately 20 acres or
less. The Missouri standard allows adjoining
20-acre field areas to be combined, to a limit

Implementing the nutrient management plan.
(Photo courtesy of USDA/NRCS)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-22

NPDES Permit Writers’ Manual for CAFOs

of 80 acres, when recommendations are within 10 percent (or 10 pounds per acre, whichever
is greater). A permit writer needs to be aware of such limitations and conditions in a technical
standard to ensure that field sizes are set appropriately in an NMP.

Timing Limitations for Land Application
The term timing limitations requires the permit writer to establish permit restrictions for land
applying manure under certain conditions. State technical standards need to identify when
applications should be prohibited or delayed. These could include, for example, times when fields
are saturated or frozen, or when other conditions prevent the use of appropriate land application
practices. Such timing limitations may be seasonal; for example, restrictions barring winter
application such as between November and February. EPA encourages CAFOs to ensure adequate
storage so that manure is never applied to frozen ground.
The term timing limitations should be distinguished from the term timing and method of land
application. Timing and method of land application refers to the availability of nutrients for crop
uptake because that can vary with the timing and the method of land application. Under the
linear approach, timing and method of land application is a term in addition to timing limitation.
Under the narrative rate approach, timing and method of land application is a factor of the
term, methodology. Timing and method of land application is further discussed in Section 6.5.2.

Outcome of the Field-Specific Assessment of the Potential for
Nitrogen and Phosphorus Transport from Each Field
Application rates for manure applied to land under the ownership or operational control of a
permitted CAFO must minimize phosphorus and nitrogen transport from the field to surface
waters using a field-specific risk assessment. 40 CFR § 412.4(c)(2)(i). Therefore, the outcome of the
field-specific assessment of the potential for nitrogen and phosphorus transport from each field (from
here forward, the term will be referred to as outcome of the field-specific risk assessment) is a term.
As previously discussed, the field-specific risk assessment should be identified in the state’s
technical standard. EPA provides examples of the different types of field-specific risk assessment
methods. Those examples are based on the risk assessment methods that were included in USDA’s
NRCS Nutrient Management Conservation Practice Standard, Code 590 (August 2006) which EPA
referenced in the 2003 CAFO rule. That NRCS practice standard describes three methods: (1) Soil
Test Phosphorus Level; (2) Soil Phosphorus Threshold Level; and (3) P-Index. Those three tools
assess the risk of phosphorus loss.4
The outcome of the field-specific risk assessment reflects the terminology typically associated with
the use of the P-Index, which reflects the risk assessment method described by the January 2012
NRCS conservation practice standards 590 and the supporting National Instruction Document
NI-190-302. NRCS conservation practice standard 590 (and elaborated on below). However, in the
CAFO rule and this Manual this phrase is to reflect the results of whichever method is required

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-23

NPDES Permit Writers’ Manual for CAFOs

by the technical standards established by the
Director, including the soil test phosphorus
method and the phosphorus threshold
method.
The field-specific risk assessment for nitrogen
evaluates whether the manure application
rate supplies excess nitrogen that could be
lost to the environment. An nitrogen loss
risk assessment should consider the nitrogen
requirement of the crop to be grown according
to the operation’s soil type, crop, and realistic
crop yields. Once the nitrogen requirement for
the crop is established, the manure application
rate is generally determined by subtracting
Terraces, buffers, and conservation tillage are among the
any other sources of nitrogen available to the
practices being used in water quality improvement projects.
crop from the crop’s nitrogen requirement.
(Photo courtesy of USDA/NRCS)
The other sources of nitrogen can include
residual nitrogen in the soil from previous
applications of organic nitrogen, nitrogen credits from previous crops of legumes, crop residues,
or applications of commercial fertilizer, irrigation water, and biosolids. Application rates are
based on the nitrogen content in the manure and should also account for application timing and
methods, such as incorporation, and other site-specific practices. 68 FR 7,211 (Feb. 12, 2003). As
long as nitrogen needs are not exceeded, the risk is assumed to be minimized.
USDA’s NRCS Nutrient Management Conservation Practice Standard, Code 590, also
recommends utilizing a leaching index to assess the risk of NO3- leaching from a field. Nitrate is
a highly mobile nutrient. As water moves through the soil profile, NO3- is not utilized by the crop
may readily leach to groundwater. ELG have not been developed for discharges to groundwater,
and therefore permit authorities are not required to write a permit term to address groundwater
contamination; however, state permitting authorities may impose NPDES permit conditions for
these discharges. 68 FR 7,216 (Feb. 12, 2003). Where surface waters have a direct hydrological
link to groundwater, a nitrogen leaching index would be an appropriate tool for the permitting
authority to include as part of the permit term. Additionally, while a nitrogen leaching index is not
a requirement under this CAFO rule, many states have chosen to make the index a state-specific
requirement in their technical standards.
If a state’s technical standard for nutrient management incorporates a version of the NRCS 590
practice standard that allows more than one assessment method, the permitting authority has the
discretion to determine which method or other state-approved alternative method may be used.
Additionally, when a standard identifies more than one allowable method, the method used at the
time of permit coverage must be used throughout the 5 years of permit coverage (unless the CAFO
permit is revised). If a CAFO operator decided to change assessment methods in the middle of

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-24

NPDES Permit Writers’ Manual for CAFOs

permit coverage, the operator would be subject to the requirements associated with a substantial
permit modification. 40 CFR § 122.42(e)(6)(iii). The field risk assessment provides CAFOs with
the information needed to determine if manure nutrients should be applied at an nitrogen or
phosphorus based application rate, or if no manure application is appropriate. Changing the tool
that is the basis for determining appropriate manure application rates is a change to the term of
the NMP and should be considered a substantial permit modification (see Chapter 4.1.7).

Soil Test
In this option, manure application rates are based on the soil test recommendations for optimum
crop production. In other words, the amount of phosphorus in the soil based on the phosphorus
soil test dictates whether the application of manure can be made to meet the nitrogen needs of
the crop, the phosphorus needs of the crop, or whether no manure nutrients should be applied.

Soil Test Example—Indiana
Indiana includes the soil test method as an option for determining application rates for
manure, biosolids, and other phosphorus­containing material, as shown in the table below.

Soil test method P risk assessment for Indiana
Soil test
phosphorus level
(Bray P1/Mehlich 3ppm)
≤ 50
51–100
101–200
> 200

Basis for nutrient application
Nitrogen based
Not to exceed 1.5 × crop P2O5 removal
Not to exceed crop P2O5 removal
No phosphorus application

Source: Indiana NRCS. 2001. Conservation Practice Standard, Nutrient Management, Code 590.
Indiana Natural Resources Conservation Service Field Office Technical Guide—July 2001.

The soil sampling depth will impact the outcome of the phosphorus soil test. According to USDAARS publication, Agricultural Phosphorus and Eutrophication, it is the top few centimeters of soil
with which surface runoff interacts. Therefore, when using soil test results for environmental
purposes, the soil sampling depth should always be considered. For more discussion on soil
sampling, see Chapter 5.

Soil Phosphorus Threshold
Many states have considered developing recommendations for phosphorus applications based
on the potential for phosphorus loss in agricultural runoff to address environmental concerns.
What makes such a determination challenging is the identification of a phosphorus soil test that
estimates when soil phosphorus concentrations becomes high enough to result in unacceptable
concentration of phosphorus enrichment of agricultural runoff. The phosphorus threshold
approach recommends nitrogen-based manure application on sites on which the soil phosphorus
test levels are below a set threshold value and phosphorus-based rates or no manure application
on sites on which soil phosphorus test levels meet or exceed the set threshold value.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-25

NPDES Permit Writers’ Manual for CAFOs

Soil Phosphorus Threshold Example—
Idaho Phosphorus Threshold (IDPTH)
The 590 conservation practice standard adopted by Idaho NRCS establishes thresholds for
determining application rates to
• Determine the method for developing the nutrient budget. This could be either crop
uptake or recommended application rate cited in the University of Idaho Crop Specific
Fertilizer Guide.
• Track trends in soil phosphorus concentrations over time and to assess environmental risk.
Soil samples taken soon after manure, biosolids or other organic by-product application could
produce erroneous soil test results for phosphorus. Soil samples taken for the Idaho Phosphorus
Threshold (IDPTH) should be delayed for 9 to 12 months after organic amendment applications.
The on-site surface or ground water resource concern will determine the appropriate depth of
the soil sample taken (Table A) for comparison to the IDPTH:
• Surface water concerns exist when surface runoff leaves the field(s) from average annual
precipitation, rain on snow or frozen ground, or irrigation.
• Groundwater concerns exist when surface water (from any source) does not leave the field.
A high water table, fractured bedrock, poor irrigation water management, cobbles, gravel,
or coarse-textured soils can contribute to downward movement of water and nutrients.*
*Note: EPA’s NPDES CAFO program does not regulate discharges to groundwater.

Table A. Required soil sample depth for the IDPTH
IDPTH soil sample depth
(inches)

Primary resource concern
Surface Water

0–12

Ground Water

18–24

When both a surface and ground water concern exist, the surface water concern governs NMP
development. If neither concern exists, the NMP is developed on the basis of the IDPTH for the
groundwater concern to maintain soil quality and long-term sustainability.
IDPTH concentrations by resource concern are listed in Table B. The primary resource concern
identified and site characteristics are used to determine the appropriate IDPTH for the site.

Table B. IDPTH concentration by resource concern
IDPTH concentration (ppm)
Primary resource concern

Olsen

Bray-1

Morgan

40

60

6

Water < 5 feet

20

25

2.5

Water > 5 feet

30

45

4.5

Surface Water
Ground Water

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

Soil Phosphorus Threshold Example—Idaho Phosphorus Threshold (IDPTH) (continued)
Table C. Phosphorus application rates based on the IDPTH
Soil test phosphorus (ppm)

Phosphorus application rate

< IDPTH

Fertilizer Guide or Crop Rotational Phosphorus uptake

≥ IDPTH

Crop Rotational Phosphorus uptake

Nitrogen-based manure applications are allowed on sites where the soil test phosphorus levels
are below the IDPTH (Tables B and C). The nitrogen availability of the planned application
must match plant uptake characteristics as closely as possible, taking into consideration
the timing of nutrient application(s) to minimize leaching and atmospheric losses. The
management activities and technologies used must effectively utilize mineralized nitrogen and
minimize nitrogen losses through denitrification and ammonia volatilization.
Phosphorus-based applications are allowed on sites where soil phosphorus levels equal or
exceed threshold values. Where phosphorus-based applications are made, the application rate
must
• Not exceed the recommended nitrogen application rate for the current crop during the
year of application.
• Not be made on sites considered vulnerable to off-site phosphorus transport unless
appropriate conservation practices, BMPs, or management activities are used to reduce
the vulnerability.
Source: Information taken from Idaho NRCS Conservation Practice Standard, Nutrient
Management, Code 590 (June 2007 version).

The Phosphorus Index5
Another approach advocated by researchers is to link critical areas of surface runoff and high
phosphorus content in a watershed. When environmental sources of phosphorus (e.g., high soil
concentrations, manure or fertilizer applications) are transported to a sensitive location (through
processes such as leaching, runoff, and erosion) water quality can be heavily impacted. A field
with high soil phosphorus levels but little opportunity for transport may not always constitute
an environmental threat, even though there is no agronomic need for additional phosphorus.
Likewise, a field where there is a high potential for transport but no source of phosphorus to
move might be of little threat. The concern and emphasis on management practices should be
focused on areas where these two conditions—phosphorus sources and transport mechanisms—
coincide. Such areas are called critical source areas.

The Concept of a Phosphorus Site Index
The purpose of the Phosphorus Site Index (P-Index) is to provide field personnel, watershed
planners, and land users with a tool to assess various landforms and management practices for
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-27

NPDES Permit Writers’ Manual for CAFOs

potential risk of phosphorus movement to waterbodies. The P-Index ranking identifies sites where
the risk of phosphorus movement might be higher than that of other sites. When the parameters
of the index are analyzed, it should become apparent that an individual parameter or parameters
could be influencing the index disproportionately. Those identified parameters can be the basis
for planning corrective soil and water conservation practices and management techniques. If
successful in reducing the movement of phosphorus, the potential for phosphorus enrichment of
surface waters will also be reduced.

The Procedures for Making an Assessment
The site characteristics addressed by the P-Index are weighted by the reasoning that some
characteristics might be more influential than others in allowing phosphorus movement from
the site. There is scientific basis for concluding that these relative differences exist; however, the
absolute weighting factors given are based on professional judgment. Examples of weighted site
characteristic factors are
▶ Soil erosion (1.5).
▶ Irrigation erosion (1.5).
▶ Runoff class (0.5).
▶ Soil phosphorus test (1.0).
▶ Phosphorus fertilizer application rate (0.75).
▶ Phosphorus fertilizer application method (0.5).
▶ Organic phosphorus source application rate (1.0).
▶ Organic phosphorus source application method (1.0).
The value categories are rated using a log base of 2. The greater the ratings, the proportionally
higher are the values. The higher the value, the higher potential for significant problems related to
phosphorus movement. Examples of value ratings are as follows:
▶ None = 0.
▶ Low = 1.
▶ Medium = 2.
▶ High = 4.
▶ Very high = 8.
To make an assessment using the P-Index, a rating value is selected for each site characteristic
using the categories NONE, LOW, MEDIUM, HIGH, or VERY HIGH. The site characteristic weight
factor is multiplied by the rating value to get the weighted value for each characteristic. The sum
of the weighted values for all eight characteristics is compared with the site vulnerability chart.
Note that each state has the ability to adopt the P-Index and make state-specific adaptations.
Some states might not consider all factors listed above, and they could weight each factor
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-28

NPDES Permit Writers’ Manual for CAFOs

differently. Therefore, ratings in each state might not follow the 0 through 8, none to very high
risk rating system. Some states might have more or fewer rating categories and use alternative
numbering systems for describing each category.
An example using the P-Index
Soil erosion (weight = 1.5) is 7.5 ton/ac/yr (= MEDIUM, value = 2)
Irrigation erosion (weight = 1.5) is not applicable (= NONE, value = 0)

1.5 x 2 = 3.0
1.5 x 0 = 0

Runoff class (weight = 0.5) is LOW (value = 1)

0.5 x 1 = 0.5

Soil phosphorus test (weight = 1.0) is 82 lb P (= HIGH, value = 4)

1.0 x 4 = 4.0

Phosphorus fertilizer application rate (weight = 0.75) is 25 lb/ac
(= LOW, value = 1)

0.75 x 1 = 0.75

Phosphorus fertilizer application method (weight = 0.5) is placed with planter
(= LOW, value = 1)

0.5 x 1 = 0.5

Organic phosphorus source application rate is 95 lb/ac (= VERY HIGH, value = 8)

1.0 x 8 = 8.0

Organic phosphorus source application method (weight = 1.0) is surface
applied a month before no-till planting (= HIGH, value = 4)

1.0 x 4 = 4.0

Sum total of all weighted values = 20.75
Site vulnerability is HIGH
Total of weighted rating values site vulnerability
< 8 LOW
8–14 MEDIUM
15–32 HIGH
> 32 VERY HIGH

Using the Phosphorus Index as a Permit Term
The phosphorus site index is the most commonly used field-specific risk assessment tool. Because
many state technical standards require the use of a P-Index for nutrient management, an
extended discussion on this risk assessment tool and its use as a permit term, is provided below.
States that use a P-Index adapt the tool to accommodate local conditions, thereby creating
variation among state phosphorus site indices (Osmond et al. 2006)].6 Some state P-Indices use a
specific risk loss category, such as low, medium or high risk, to describe the quantitative weighted
value of the risk. In others, only the quantitative weighted value is used to describe the risk. In
many states, an appropriate application rate basis (such as nitrogen-based, phosphorus-based,
or no application) is also applied to each risk. When a state’s P-Index is used as the field-specific
risk assessment tool, it is important that the permit term include the risk and the recommended
nutrient basis for land application.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-29

NPDES Permit Writers’ Manual for CAFOs

Two different risk categories may have the
same recommendation for land application.
For instance a state could recommend
nitrogen-based manure application for
fields that have low risk and medium risk for
phosphorus transport. Even if the application
rate basis for a field does not change with a
change in the risk rating, the operator (or
planner) needs to know when the risk for a
field is increasing. The reason for this is that
any increase to the outcome of the field-specific
risk assessment is a substantial change to a
term that necessitates a permit modification.
Even though both low and medium risk
ratings might recommend an nitrogen-based
Scientist notes excellent corn growth on manured soil treated
with alum residue, which cuts phosphorus losses in runoff
application rate, the change from low to
water. (Photo courtesy of USDA/ARS)
medium is indicative of some other change in
the current management or conditions on the
field, which is resulting in an increased risk of
phosphorus runoff. Therefore, the permit term
needs to capture the risk category or other rating in addition to specifying the recommended
application rate basis.
The factors that are considered in calculating a P-Index often include variables that fluctuate over
time, such as application rates and methods of application for inorganic and organic nutrient
sources, the timing of each application, conservation practices implemented or the actual
crops planted (among others). Those variables can fluctuate with each crop grown on a field
and also depend on how and how often manure is applied. Over the course of a 5-year permit
cycle, a P-Index risk rating could theoretically fluctuate from a low to high risk on a single field.
The linear approach inherently accommodates the variation in risk over the life of the permit
because the NMP reflects the actual crops and associated manure application rates that will be
used. The narrative rate approach allows that implementation of the NMP could differ from what
was anticipated when the plan was written. Methods of nutrient applications might fluctuate or
nutrient applications might occur at different times than when they were originally planned,
particularly if crop rotations change (as is accommodated under the narrative rate approach).
Given those anticipated changes, a field’s actual risk for an individual crop year might change
during the period of permit coverage and might not reflect the risk that was calculated at the
beginning of the permit cycle. That situation could require permit modifications during the
5-year permit term, depending on how the outcome of the field-specific risk assessment is written
as a permit term.
The outcome of the field-specific risk assessment is required to be reported by field, but not for each
individual crop grown in the field. Nevertheless, even though the permit term is not crop-specific,

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-30

NPDES Permit Writers’ Manual for CAFOs

the outcome of the assessment depends on the management of each specific crop (i.e., accounting
for the manure application rate and method for each crop) and, thus, is indirectly crop specific.
This Manual describes two possible methods for developing the term outcome of the field-specific
risk assessment. In the first method, the term reflects the field risk for each crop-year in the plan.
This method is described as multiple risk levels over the planning period. That method meets the
CAFO rule requirement for reporting the risk for each field for each year covered by the NMP but
restricts the operator in the sense that any management changes during the planning period must
maintain the risk identified for each crop-year. This method aligns with the requirements of the
linear approach.
In the second method, the term is described as a single risk level for a field over the entire
planning period. It is based on the highest risk calculated for any individual crop year. This
method accounts for the inherent relationship between the P-Index and the management of
each crop and allows each individual year’s risk to fluctuate as long as the highest risk over the
planning period is not exceeded. This second approach reconciles inconsistencies between the
multiple risk level method and the flexibility intended by the narrative rate approach.
It is important to note that, while EPA has determined that the two methods described below
are consistent with the requirements of the CAFO rule, they are not necessarily the only
valid methods for capturing the term outcome of the field-specific risk assessment. Permitting
authorities may identify other approaches consistent with the regulatory requirements.
As mentioned above, the single risk level approach accommodates the flexibilities provided
under the narrative rate approach. Unlike the linear approach, the narrative rate approach
allows CAFOs to adjust their manure nutrient application rates without requiring the permit
to be modified. 73 FR 70,449 (Nov. 20, 2008). The predicted form, source, amount, timing and
method of application of manure, litter and process wastewater set forth in the NMP are not
permit terms under the narrative rate approach so the actual inputs may differ from what was
projected in the NMP. Additionally, the narrative rate approach allows the flexibility to include
alternative crops that might be planted over the course of the permit. Because changing any of
those inputs could result in a change to the risk in an individual crop year, the single risk level
approach sets the permit term as the highest risk (i.e., the risk that results in the most stringent
nutrient basis for land application) anticipated over the course of permit coverage. Actual
inputs for factors such as the crop planted or the form, source, timing and method of nutrient
application can fluctuate, as anticipated under the narrative rate approach, as long as the field’s
risk for any individual crop year does not increase above this highest predicted rating. That
avoids the requirement for a permit modification based on a substantial change to the NMP that
might otherwise be needed if the permittee is restricted to the risk predicted in the NMP for
each individual crop year. The implications of this approach with respect to the allowable land
application rates are discussed in Section 6.5.3 under the discussion on the maximum amount of
nitrogen and phosphorus from all sources.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-31

NPDES Permit Writers’ Manual for CAFOs

Example of two approaches to expressing the term outcome of the
field-specific risk assessment for nitrogen and phosphorus transport
In a CAFO’s NMP, Field A results in the following risk ratings and associated nutrient basis for
land application for a corn-soybean rotation.
Crop Year 1: Medium—Nitrogen-based application
Crop Year 2: Medium—Nitrogen-based application
Crop Year 3: High—Application at 1.0 x crop phosphorus removal rate
Crop Year 5: Medium—Nitrogen-based application

Method 1 (Multiple Risk Levels)
The permit term could be reported for every year on every field. Under this approach, the field
will have multiple risks, each corresponding to a particular crop year.
Field

1

Year

Crop

Risk

Recommended rate basis

2010

Corn

Medium

Nitrogen-based Application

2011

Soybean

Medium

Nitrogen-based Application

2012

Corn

High

1 times crop phosphorus removal

2013

Soybean

High

1 times crop phosphorus removal

2014

Corn

Medium

Nitrogen-based Application

Under the multiple risk method, where the permit term includes the individual risk for each
crop year under permit coverage, the operator must not exceed a medium risk in crop years
1, 2 and 5 and a high risk in crop years 3 and 4. For example, the operator could substitute an
alternative crop in Year 1, which allows a higher manure application rate as long as the change
does not cause the risk rating to increase to high in year 1 year 2, or year 5.

Method 2 (Single Risk Level)
The permit term could be reported as a single risk for the field. In this case, the highest risk
rating for the field for the planning period (usually corresponding to a 5-year permit period)
would be reported as the permit term.
Field

Risk

Recommended rate basis

1

High

1 times crop phosphorus removal

Under the single risk method, the term would reflect the high risk rating for the entire permit
period. The operator would have more flexibility to make changes in years 1, 2, and 5 that
might increase the risk rating as long as the change does not cause the risk rating to exceed
the high risk in any year.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-32

NPDES Permit Writers’ Manual for CAFOs

Additional Considerations for Implementing the Outcome of the FieldSpecific Risk Assessment when Utilizing a Phosphorus Site Index
In many states, an appropriate application rate for manure (e.g., nitrogen-based, phosphorusbased, or no application) is associated with the risk estimated by a state-specific P-Index.
Additionally, many state P-Indices include the planned application rate of manure as a variable
in calculating the risk in the P-Index. A CAFO’s planned application rate could result in a risk
rating that would not recommend the planned rate to be applied. Planned rates of manure
application must always align with the recommended rate associated with the estimated risk.
Therefore, determining the appropriate land application rate is an iterative process because it is
necessary to analyze the planned rate of manure application in the calculation of the P-Index
until the planned rate aligns with the recommend rate as defined by the P-Index. An example is
given below.
A state-specific P-Index is as follows:
P-Index rating

Risk

Recommended nitrogen and phosphorus
application rates

0–5

Low

Nitrogen-based

6–10

Medium

11–15

High

Crop phosphorus removal
No application

An operator may plan to apply manure at an nitrogen-based rate on his field the first year
of operation. When the P-Index is calculated, which takes the nitrogen-based rate into
consideration, the P-Index rating is 7, and the risk for runoff is medium. The recommended
application rate for manure, when the risk is 7 should not exceed the crop phosphorus removal
rate. The planned nitrogen-based rate does not align with the recommended rate. The P-Index
indicates that an nitrogen-based manure application increases the risk for phosphorus runoff on
this particular field and therefore should not be applied. The rate needs to be adjusted to lower the
risk. (Another variable influencing the risk could also be adjusted or conservation practices could
be implemented that would also reduce the risk to low, and then the planned nitrogen-based rate
could be applied because it would align with the recommended rate, but this example assumes
that other factors are held constant.)
No matter how the term for the outcome of the field-specific risk assessment is identified in the
permit, planned rates of application should not exceed the recommended rates based on the
P-Index or other risk assessment method used.

Planned Crop or Other Use
An NMP is predicated on the use of manure as a source of nutrients for a crop. Land application
of manure that is not intended for crop uptake is simply waste disposal. Without a crop to actively
utilize nutrients and prevent erosion, nutrients applied in manure can be washed directly into
surface streams or leached into the groundwater. The vegetative cover that a crop provides
reduces the potential for runoff and erosion from an area. The root system of a crop holds soil
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-33

NPDES Permit Writers’ Manual for CAFOs

together and provides a network of openings,
or pores, for water to infiltrate soil rather than
run off. When selecting a crop, the operator
should consider factors including:
▶ Adaptation to the local climate.
▶ Ability to use nutrients when manure
applications are made.
▶ Harvest requirements.
▶ Marketability and profitability.
▶ Yield.
▶ Suitability to soil conditions.
▶ Pest management.

Crops growing in a Missouri field. (Photo courtesy of USDA/
MO NRCS)

Among the most common cropping practices
that receive manure applications are a corn/
soybean rotation (i.e., corn is grown in one year and soybeans the next year), continuous corn (i.e.,
corn is grown every year), a corn/soybean/wheat rotation (i.e., three crops are grown in 2 years),
and forage (i.e., hay or grass). Yet depending on the region, manure application is commonly used
for many different crops. Specific data about the appropriateness of manure application and local
application rates should always be outlined in the state’s technical standards and often follow
the guidance of local agronomists, NRCS experts, a Cooperative Extension Service, or land grant
university. Those experts help operators select sustainable cropping practices, and they make
nutrient application recommendations.
A CAFO’s NMP must identify the crop or crops that are planned for each field for every year of
permit coverage. Alternate crops may be specified for NMPs developed using the narrative rate
approach, as described in Section 6.5.3.

Crop Rotations and Crop Nutrient Requirements
To develop appropriate land application practices, CAFOs should identify planned crop rotations.
A rotation is the growing of a sequence of crops to optimize yield and crop quality, minimize the
cost of production, and maintain or improve
soil productivity. CAFOs should describe their
Benefits of Crop Rotations
planned sequence of crops (e.g., corn for silage,
A cropping sequence with a variety of
soybeans) preferably for 5 years. That should
crop types (grasses, legumes) and rooting
characteristics (shallow roots, deep
include planting and harvesting dates and
roots, tap roots) better uses available soil
residue management practices. Crop rotation
nutrients. Following a shallow-rooted crop
is important in calculating total nutrient needs
with a deep-rooted crop helps scavenge
over the period of the rotation, nutrient buildup,
nutrients that might have moved below
and nutrient removal via harvesting.
the root zone of the first crop.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-34

NPDES Permit Writers’ Manual for CAFOs

Realistic Annual Yield Goals
The realistic yield goal is the estimated potential for crop yield for a given field. The total nutrient
requirements for fields are largely based on the CAFOs expected crop yields; generally, the higher
the yield expectation, the higher the nutrient requirement. An unrealistic estimate can result in
either a deficiency or an excess of nutrients being applied. In addition to crop variety and climate,
crop yields are influenced by field-specific factors including, among others, soil fertility, soil type,
crop management and, pest control. Thus, estimated yields can be expected to vary for different
fields. State technical standards for nutrient management need to identify acceptable methods
and data sources for establishing realistic yield goals.
The best way to estimate yield potential is to consider production practices given the relationship
between crop yields and site-specific management and field conditions. For example, the average
of the three highest yields of the five most recent years that the specific crop was grown in the
field could be used. Increased yields from the use of improved varieties and hybrids should be
considered when yield goals are set for a specific field.
Where records are not available, as is the case with most new operations, another method
of estimating yield is needed. NRCS, in conjunction with state agricultural and Cooperative
Extension Service specialists, establish realistic yields for specific crops on different agricultural
soils. Those values are based on inherent soil properties and long-term observations. They
should be viewed only as estimates because they might not reflect irrigation, new cultivars, and
improved management tools. That information is available through county NRCS field offices.
Local farmers, fertilizer dealers, and custom harvest companies might also be able to provide
yield data. Field-to-field and farm-to-farm differences can easily result in a ±20 percent difference
in realistic yield expectations from those published by state and Cooperative Extension Service
specialists and should be considered normal. Further differences might also exist because of
practices such as supplemental irrigation or no-till planting although local specialists might have
information to document those differences.
States should establish in their technical standards criteria for deriving realistic yield goals
including criteria for adjusting yield goals according to actual crop yields. CAFO operators of
Large CAFOs subject to subparts C and D should follow the criteria established in the techni­
cal standards for deriving a realistic yield goal for a given crop. CAFO operators must follow the
criteria in the technical standards and should have sufficient data and records to demonstrate that
the yield goals used as the basis for developing application rates are realistic. 40 CFR § 412.4(c)(2).
The permit term for realistic annual yield goal is the yield goal identified in the NMP for each crop
grown in each field for each year of the planning period. See 40 CFR sections 122.42(e)(5)(i)(A) and
122.42(e)(5)(ii)(A).
While the basis for establishing the yield goal is not part of the permit term, EPA recommends
that the basis (e.g., historical records, data source for book values) be identified in the NMP. In any
event, the permitting authority has the authority to request the basis for the yield goal that was
used. 40 CFR § 122.23(h). Additionally, upon subsequent permit issuance, the public will have
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-35

NPDES Permit Writers’ Manual for CAFOs

the opportunity to review yield goals in light of actual yields reported by the CAFO in its annual
reports. Id.; § 122.42(e)(4)(viii).
Once a realistic yield expectation is determined for a crop, the amount of nutrients required to
achieve that yield can be determined.

Total Nitrogen and Phosphorus Recommendations for Each Crop
A key factor in determining the amount of manure to apply to a crop is the amount of nitrogen
and phosphorus required for a crop to achieve a given yield. The total nitrogen and phosphorus
recommendation for specific crops should be identified by each state’s technical standards for
nutrient management.
While the total amount of nutrients required to achieve a given yield may be met by drawing
from all available sources, recommendations for a crop might or might not account for available
nutrients already present in the soil. State recommendations may be based solely on quantity
of nutrients needed to achieve the given yield goal or may be based on the amount of nutrients
needed in addition to those available to a crop from the soil needed to achieve the given yield
goal. The latter is commonly referred to as the crop’s fertilizer recommendation. Fertilizer
recommendations can account for the availability of existing nutrients and how nutrients
(existing and added) will behave with time, management practices, and other environmental
conditions that affect their availability to a plant. Phosphorus fertilizer recommendations
account for existing available nutrients and, therefore, must always consider the results of a
soil analysis. That is less common for nitrogen fertilizer recommendations because nitrogen
compounds are highly mobile and undergo rapid transformations in soil (see Section 6.1.1 on the
nitrogen cycle). Providing an accurate and representative soil analysis of plant available nitrogen
is more difficult than for phosphorus because the samples need to be taken close to the time
when nutrients will be land applied. Therefore,
nitrogen fertilizer recommendations often
represent the entire quantity of plant available
nitrogen needed from all sources to achieve the
yield goal.7
Instead of using a fertilizer recommendation
to quantify the nutrients needed to achieve
a certain yield, some technical standards
express the total nitrogen and phosphorus
recommendation in terms of the crop’s nutrient
removal rate. When a crop is harvested, the
nutrients in the harvested portion of the plant
that the crop extracted from the soil, are
removed from the field. Standard values have
been calculated for specific crops to quantify
the amount of nutrients removed on the basis

Cropland fertilized with hog manure. (Photo courtesy of
USDA/NRCS)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-36

NPDES Permit Writers’ Manual for CAFOs

of the yield unit that is harvested. Crop yield units for the most common grain and forage crops
are bushels/acre and tons/acre, respectively. The nutrient content of common crops is shown in
Table 6-2 . The values in Table 6-2 are generalized national data. Local crop nutrient content is
not expected to differ greatly from that shown in Table 6-2 but should be based on local NRCS,
Cooperative Extension Service, or land grant university data. Such local data should be used for
planning purposes. A crop’s nutrient removal rate is determined by multiplying the nitrogen or
phosphorus per yield unit by the expected yield.

Nitrogen
Total nitrogen recommendation is almost always based on the fertilizer recommendation. The
recommendation defines the amount of nitrogen needed by the crop and application rates are
derived considering the various sources of nitrogen available to meet the total nitrogen need.
The exception to that approach is when the crop is a legume. Legumes can supply and meet
their own nitrogen needs through nitrogen fixation. However, some states’ technical standards
allow for manure to be applied to legumes, because legumes will use nitrogen that has been
supplied externally to the extent that it meets the plant’s needs, rather than fixing nitrogen to
meet that need. In states that allow manure application to legumes, typically it is allowed at the
crop’s removal rate. The nitrogen removal rate will determine the amount of nitrogen expected in
harvested biomass for a given crop and yield. Where states allow that, the nitrogen removal rate
can be reported for legume crops as the crop nitrogen recommendation. In all other cases, the
crop nitrogen fertilizer recommendation should be used.

Phosphorus
Total phosphorus recommendations can follow either the phosphorus removal rate or the
phosphorus fertilizer recommendation (based on the soil phosphorus test level). When the
soil test for phosphorus is low, operators will most likely follow the phosphorus fertilizer
recommendation, rather than the removal rate, because it allows a higher phosphorus application
rate, which will build up the soil phosphorus level to improve the fertility of the field. When the
phosphorus fertilizer recommendation is followed, the soil test level increases with time, and
subsequently the phosphorus recommendation should decrease.
The phosphorus fertilizer recommendation is based on the amount of phosphorus that is needed
beyond what is already available in the soil to grow a given yield of a specific crop. A soil sample
is analyzed to determine the amount of phosphorus that can be removed from the sample; the
ability to remove phosphorus from the sample represents the plant availability of phosphorus.
Fertilizer recommendations based on soil test phosphorus levels are designed to achieve an opti­
mum available soil phosphorus level (see Figure 6-7 and Section 5.9.3 Soil Test Protocols). When
the soil test is low, the recommendation is to apply more than what the crop will remove with
the intention to build up the soil test level so that the soil can supply the crop and subsequent
crop’s phosphorus need. Conversely, when the soil test level is high, the recommendation is less
than the removal rate because the intention is to draw down the phosphorus level in the soil to
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

achieve an optimum level. When the phosphorus fertilizer
recommendation is used as the term for total phosphorus
recommendation, the term will inevitably change because
the intent of the recommendation is to increase the
amount of phosphorus in the soil (or to decrease the
amount of phosphorus in soil when soil tests are high) to
achieve an optimum level of phosphorus soil fertility.
An application based on a crop phosphorus removal
rate will maintain the current soil phosphorus test level
because the removal rate supplies only enough phosphorus Figure 6-7. Yield response curve illustrating the
soil test interpretation levels.
to replace the phosphorus that is removed with harvest.
The amount of plant available soil phosphorus will have
no bearing on the amount of additional nutrients to apply.
When the crop phosphorus removal rate is used as the term for total phosphorus recommendation,
the term will be consistent over time for a specific crop unless the crop yield goal is adjusted.
Figure 6-8 provides an example of how the recommended pounds of P2O5 to apply can differ when
following either a soil test fertilizer recommendation or a crop phosphorus removal rate.
The site-specific information captured for the term, total nitrogen and phosphorus recommendations
for each crop, will depend on what the state’s technical standards require. In many cases, the state’s
technical standards will allow for either the fertilizer recommendation or the crop removal rates,
in which case, the higher rate will typically be used to calculate manure nutrients to be applied.

Nutrients removed in harvested portions
of corn silage.

Phosphate (P2O5) recommendations
for corn silage.

Nutrient removed
per unit of yield
P2O5
Crop

Unit of yield

Yield potential—tons per acre
Soil test

K 2O

lb/unit

22
24
26
lb P2O5 per acre

28

115

125

130

135

140

90

100

105

110

115

65

75

80

85

90

35 (70)

35

40

40

45

45

40 (80)

0

0

0

0

0

5 (10)1

Corn
Silage

20

ppm (lb/acre)

10 (20)
ton

3.30

8.00

15-30 (30-60)

1
2

2

Values in parentheses are lb/acre.
Maintenance recommendations are given for this soil test range.

Figure 6-8. Removal rates versus fertilizer recommendations. (Source: TriState Fertilizer
Recommendations)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

Understanding Substantial Changes with
Low Phosphorus Soil Test Results
Various applications for the result of the soil phosphorus analysis are discussed throughout this
chapter, which include how they are applied in deriving:
• Outcome of the field-specific risk assessment.
• The total phosphorus recommendation for each crop.
• The maximum amount of phosphorus to be applied.
• The methodology (under the narrative rate approach).
With respect to the above terms, any changes to the field-specific maximum amounts of phosphorus
and any changes that are likely to increase the risk of nitrogen and phosphorus transport to waters of
the U.S. as determined by the outcome of the field-specific risk assessments are substantial changes to
the terms of an NMP.
As just discussed, when soil tests are low, the operator will likely follow the phosphorus fertilizer
recommendation over the removal rate if given a choice. Following the fertilizer recommendation
will increase the soil test value and subsequently decrease the corresponding fertilizer
recommendation.* Thus, over a period the permit term, total phosphorus recommendation, is likely to
change.
In many cases, when the phosphorus soil test is low, the risk for runoff will also be low and manure
will most likely be applied at an nitrogen-based rate. As a result, the phosphorus recommendation is
likely to be become obsolete. The phosphorus fertilizer recommendation is not followed when land
applying using an nitrogen-based rate. While the fluctuating term, total phosphorus recommendation
would be considered a permit modification, it has no bearing on the maximum amount of phosphorus
that can be applied and thus it would not be a substantial permit modification.
However, it is possible for a field to have a high risk for runoff (generally limiting application to a
phosphorus-based rate) and a low phosphorus soil test. In this case, the fertilizer recommendation
is most likely followed. In this case, the maximum amount of phosphorus will be the amount directly
determined by the fertilizer recommendation. Over time, the phosphorus soil test will increase
and subsequently the fertilizer recommendation will decrease. Because that field has a high risk for
runoff, as the recommendation declines, less phosphorus should be applied, thereby decreasing
the maximum amount of phosphorus that can be applied. With every change to the total phosphorus
recommendation (in this case the fertilizer recommendation), the maximum amount of phosphorus
changes triggering a substantial permit modification. EPA believes that is necessary to ensure that
phosphorus is not over-applied as the soil phosphorus levels build on such high-risk sites.
*Note:
There are many ways to read a soil test analysis, which could lead to confusion when discussing the change
to the fertilizer recommendation. Phosphorus fertilizer recommendations are typically given as the pounds of
phosphorus to be applied to a crop for a given soil test range. Therefore, for a range of soil test results, the
recommendation will be the same. For example, a quantitative range of soil test results (i.e., 0–50, 50–100,
100–150 ppm) will be qualitatively described (0–50 = low, 50–100 = optimum, 100–150 = high). Different
phosphorus recommendations for the amount of additional phosphorus to be applied will be provided for each
qualitative soil test range. If a soil test is taken more than once over the course of a 5-five year permit term, a
change to the crop recommendation term would occur only if a new soil test recommendation is applied.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.1. Site-Specific Terms: Linear and Narrative Rate Approaches

6-39

NPDES Permit Writers’ Manual for CAFOs

6.5.2. Additional Site-Specific Terms: Linear Approach
Because the linear approach specifies the maximum amount of nutrients that will be supplied
from manure, the permit must include terms for the variables and data that are used to derive that
value. In addition to the terms that apply to both approaches, which are discussed in Section 6.5.1
above, the CAFO regulations require the terms described in this section for application rates
expressed using the linear approach.

Credits for Plant Available Nitrogen in the Field
Once the nitrogen recommendation for a crop is known, the manure application rates can be
determined by subtracting from the total nitrogen recommendation the amount of nitrogen
that will be available to the crop from all other sources. One of these sources is nitrogen that is
already in the field. These in-field nitrogen sources of PAN are referred to as nitrogen credits. Two
common credits for PAN are organic nitrogen from prior manure applications that mineralizes
to available nitrogen compounds over the course of the planning period and nitrogen supplied
from legume crops. Quantifying these sources of PAN is part of the methodology for calculating
application rates for the narrative rate approach and a permit writer should ensure this is
specified in the NMP. Under the linear approach, the credits themselves are a term.

Nitrogen Credits from Mineralization
Not all nitrogen in manure that CAFOs apply is available to the crop during the year of
application. Some nutrients require organic material decomposition before they are available for
plants. An accurate estimate of the amount of organic nitrogen that will become available in the
years after a manure application event is considered a part of the credits for PAN in the field. The
availability of organic nitrogen from manure application will vary according to the degradability
of organic nitrogen compounds in the manure and other environmental conditions. Organic
nitrogen in different types of manure (e.g., dairy, poultry, beef) mineralizes at different rates.
Varying environmental conditions associated with the timing of application (fall versus spring),
such as soil temperature and moisture, affect the ability of microorganisms to mineralize organic
nitrogen compounds in the manure into plant available forms. Availability coefficients are
applied to the amount of organic nitrogen, as determined from the manure analysis. Coefficients
typically are used for calculating nitrogen availability in the first, second and third year after
application. (See section 6.1.1 and Appendix A, Basic Soil Science and Soil Fertility, for more
details on the nitrogen cycle and nitrogen mineralization.)
State technical standards should provide mineralization coefficients that are based on the type
of manure being applied and the time of year that application is occurring. Most states consider
nutrients to be 50 to 75 percent available in the first year. Typical rates are provided in Table 6-4,
but state-specific rates should be reflected in a CAFO’s NMP.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-40

NPDES Permit Writers’ Manual for CAFOs

Table 6-4. General mineralization rates for nitrogena
Years after initial application
1
Waste and management

2

3

Percent available (accumulative)

Fresh poultry manure

90%

92%

93%

Fresh swine or cattle manure

75%

79%

81%

Layer manure from pit storage

80%

82%

83%

Swine or cattle manure stored in covered storage

65%

70%

73%

Swine or cattle manure stored in open structure or
pond (undiluted)

60%

66%

68%

Cattle manure with bedding stored in roofed area

60%

66%

68%

Effluent from lagoon or diluted waste storage pond

40%

46%

49%

Manure stored on open lot, cool-humid

50%

55%

57%

Manure stored on open lot, hot-arid

45%

50%

53%

Source: Table 11-9, USDA-NRCS, 1999
a. Table assumes annual applications on the same site. If a one-time application, the decay series can be
estimated by subtracting year 1 from year 2 and year 2 from year 3. For example, the decay series for fresh
poultry manure would be 0.90, 0.02, 0.01. The decay rate becomes essentially constant after 3 years.

The permit writer should be aware that the estimate for residual manure nitrogen in the field,
which, in the linear approach, contributes to the permit term, credits for PAN in the field is
estimated from the manure analysis used to develop the NMP. Therefore, the requirement for
Large CAFOs to sample and analyze their manure annually could result in changes in the value
of PAN in the field. Medium and Small CAFOs are subject to BPJ requirements and might be able
to account for the nutrient content of manure using standard book value estimates. Standard
estimates will not reflect fluctuations of the manure analysis and associated changes to the PAN
credits in the field. The narrative rate approach accommodates for those types of fluctuations.
Temporal fluctuations in the manure nutrient content can be great for uncovered lagoons and
pits because seasonal variations in temperature and precipitation can alter nutrient content
through dilution, evaporation, and volatilization. Manure analyses from under-barn concrete
pits or covered aboveground tanks will not vary as much because there is limited exposure to the
environment.

Nitrogen Credits from Legumes
As described in the discussion above on total nitrogen recommendations, legumes can fix
atmospheric nitrogen to supply their own nitrogen need and add nitrogen to the soil. The state’s
technical standards for nutrient management need to describe how to account for nitrogen
credits from a previous legume crop so the NMP can properly account for them. Two examples
from Montana and Iowa are provided below. Montana’s technical standard provides legume
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-41

NPDES Permit Writers’ Manual for CAFOs

credits that vary with plant species and growing
conditions (Table 6-5):
Iowa’s technical standard sets an upper limit of
total nitrogen credits that can be derived from a
soybean crop. Credits for nitrogen that are to be
carried over into the following year are calculated
as follows:
▶ Last year’s soybean crop: 1 lb nitrogen per
bushel of yield, maximum of 50 lb nitrogen
per acre credit.
▶ Legume forage crop:
■ Last year’s crop with 50 to 100 percent
alfalfa or other legume in stand:
100 to 140 lbs nitrogen per acre.
■ Last year’s crop with 20 to 50 percent
alfalfa or other legume in legume/grass
mixture: 50 to 80 lbs nitrogen per acre.
■ Two years ago crop with 50 to 100 percent
alfalfa or other legume in stand: 30 lbs
nitrogen per acre.
▶ Last year’s legume green manure crop:
100 lbs nitrogen per acre.

Table 6-5. Legume nitrogen credits for Montana
Nitrogen fixation
(lbs/acre)*

Legume
Alfalfa (after harvest)

40–80

Alfalfa (green manure)

80–90

Spring Pea

40–90

Winter Pea

70–100

Lentil

30–100

Chickpea

30–90

Fababean

50–125

Lupin

50–55

Hairy Vetch

90–100

Sweetclover (annual)

15–20

Sweetclover (biennial)

80–150

Red Clover

50–125

Black Medic

15–25

* The maximum nitrogen fixation in lbs/acre should be used
unless appropriate justification is given showing lower
nitrogen fixation is appropriate. In all cases, the nitrogen
fixation used must be within the ranges specified above.

Nitrogen credits are a term even for a field with
a phosphorus-based rate because the nitrogen
credit is needed to calculate the appropriate
amount of supplemental nitrogen to be added
to the field to ensure that the crop’s nitrogen
requirement is not exceeded.

Consideration of Multi-Year
Phosphorus Application
A multi-year phosphorus application consists
of applying a single application of manure at
a rate equal to the recommended phosphorus
application rate (whether based on soil test
levels or crop removal) for multiple years in
the crop sequence. In some situations a multiyear phosphorus application is used because
the application equipment might not be able

An example of no till farming where young soybean plants
thrive in the residue of a wheat crop.
(Photo courtesy of USDA/NRCS)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-42

NPDES Permit Writers’ Manual for CAFOs

to apply manure at the recommended phosphorus application rate because that rate is lower
than the spreading capability of the equipment. In other cases, it might be more practical and
economical to bank phosphorus by applying manure at rates higher than the crop’s phosphorus
needs for that year.
The use of multi-year phosphorus application is a flexibility that the Director can provide to CAFOs
when establishing the state’s technical standards for nutrient management. 40 CFR § 412.4(c)(2)(ii).
However, that flexibility is allowed only on fields that do not have a high potential for phosphorus
runoff to surface waters. Id. Such flexibility is not needed when the outcome of the field-specific
risk assessment permits an nitrogen-based application rate because an nitrogen-based application
rate already provides 2 to 4 times the amount of phosphorus that a crop typically needs. Therefore,
consideration of multi-year phosphorus application will never be a term for any field with an
nitrogen-based limit. It is a flexibility to be considered once the outcome of the field-specific risk
assessment restricts application to a phosphorus-based rate.
The term for consideration of multi-year phosphorus application should identify the field, crop,
and year that the multi-year phosphorus application will occur. Because a multi-year phosphorus
application should never exceed the annual nitrogen rate for the year of application, the plan
should demonstrate that the amount of nitrogen being applied does not exceed the allowable
nitrogen recommendation for that crop during the year that the multi-year phosphorus
application is made.
When a multi-year phosphorus application is allowed, CAFOs must not apply additional
phosphorus to those fields until the amount applied in the single year has been removed through
plant uptake and harvest. 40 CFR § 412.4(c)(1). Therefore, the permit writer should ensure that no
manure application is planned for the number of years covered by the multi-year application. The
number of years will depend on how many years’ worth of phosphorus was applied in a single
application [68 FR 7,210 (Feb. 12, 2003)].

Accounting for All Other Additions of Plant Available Nitrogen and
Phosphorus
For many fields where manure is land applied, other sources of nutrients are also land applied.
The term, accounting for all other additions of plant available nitrogen and phosphorus, is to
capture those sources of nutrients. The nutrient sources can include chemical fertilizers, biosolids,
nutrients in water used for irrigation, or any other additions to the field but would not include
mineralization of nitrogen from previous land application events or legume nitrogen credits.
Pound for pound, animal manure does not have the same nutrient value as commercial fertilizer,
and commercial fertilizer can be customized and blended to meet specific nutrient requirements.
Farmers often supplement animal manure applications with commercial fertilizer or biosolids.
Furthermore, because animal manure contains relatively high concentrations of phosphorus,
crops are generally not supplied with enough nitrogen when manure is applied on a phosphorus

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-43

NPDES Permit Writers’ Manual for CAFOs

basis. Therefore, CAFOs might need commercial nitrogen fertilizer to meet the crop’s total
nitrogen requirements when manure is applied at less than the nitrogen rate.
Irrigation water, especially from shallow aquifers, contains some nitrogen in the form of NO3-N.
Also, water from runoff ponds and storage lagoons contains nutrients. CAFOs must include
those nutrient sources in the NMP. To calculate the amount of nitrogen applied with irrigation
water, CAFOs must conduct a nutrient analysis to determine the concentration of nitrogen and
phosphorus in the water, typically reported as NO3-N and soluble phosphorus in ppm or mg/L.
The permit term is not the actual amount of the nutrient source to be applied the field. The CAFO
rule describes the term as accounting for additions of plant available nutrients to indicate how
those other nutrient sources are included as additions for meeting crop needs. That is to say that
they must be identified in the NMP, and the amount of nutrients they contribute must be included
in the calculation of the total nutrients to meet the nutrient recommendation. Therefore, while
the permit term could be captured in the permit as a specific type of fertilizer, the actual amount
of fertilizer applied can fluctuate year to year. The plan should include the nutrient content of the
sources that are accounted for (e.g., the N-P-K value of supplemental fertilizer or the nitrogen and
phosphorus concentration in biosolids or irrigation water).

Example term accounting for all other additions
of plant available nitrogen and phosphorus
A Large permitted CAFO plans to apply 100 lbs/acre of nitrogen from manure and 50 lbs/acre of
nitrogen from a 25­0­0 commercial fertilizer to Field A in each year of the permit.
The permit term for accounting for all other additions of plant available nitrogen and phosphorus
means that the plan includes the additions of commercial fertilizer to field A. (For an illustration,
see the example provided in section 6.6.2 under Accounting for all other additions of plant
available nitrogen and phosphorus.) In year 2 of the permit, the manure test indicates the
concentration of nitrogen in the manure has decreased because of a change in the feed ration.
Using all the manure generated at the CAFO supplies only 90 lbs/acre of nitrogen, and the
amount of commercial fertilizer used must be increased. That is an acceptable change to make
because the actual amount of fertilizer being applied is not the permit term. However, if the
CAFO operator wanted to use biosolids to supplement the nitrogen supplied by manure this
would be considered a change to the NMP and would need to be submitted to the Director
because that source was not accounted for in the NMP.

Form and Source of Manure that Is Land Applied
The form and source of manure are closely related. The form of manure will dictate the type
of storage structure or source. The form and source of manure are required terms for the linear
approach because they relate to the method of application, which is also a term and is discussed
in more detail below. 40 CFR § 122.42(e)(5)(i)(A).

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-44

NPDES Permit Writers’ Manual for CAFOs

An automated lagoon waste management
system for a 900-head hog farm.
(Photo courtesy of USDA/NRCS)

Manure handled as a solid, such as broiler and turkey
manure, is typically surface applied to cropland using
either tractor-drawn or truck-mounted, box-type manure
spreaders. Manure handled as a semi-solid or slurry, such
as dairy cow manure removed from free-stall barns by
scraping, is typically applied to cropland using tractordrawn or truck-mounted tanks. That type of manure
typically can be surface applied and incorporated into
the soil by disking or plowing, or can be directly injected
into the soil. Manure handled as a liquid, such as lagoon
wastewater, could be applied to cropland using tractordrawn or truck-mounted tanks or irrigation systems.
Because of the volume of manure when handled as a liquid,
irrigation is a fairly common method for land application of
this form of manure because it reduces labor requirements.
Liquid manure is either applied on the soil surface and
incorporated shortly after application or can be directly
injected into the soil. Incorporation or injection helps to
control loss of volatile ammonia and odors. Incorporation
is very effective at controlling runoff of manure nutrients
from land application if done within a few hours after
application. A soil injector applies liquid manure directly
into the soil to a depth of 6 to 9 inches as the tanker passes
over the field.

The term form refers to the form of the manure (solid, semi-solid, slurry, and liquid) and the term
source refers to the storage structure containing the manure. Multiple applications of manure can
be made to a single field in one season. Each application could come from a different source and
be of a different form. For example, in March solid manure from a manure stack might be land
applied to a field. That same field could receive an additional manure application the next month
in the form of an injection of liquid manure from a lagoon. Each form and source of manure
application should be identified in the NMP and as the permit term for form and source of manure
in the linear rate approach.

Timing and Method of Land Application
The timing and method of land application of manure have a direct impact on the amount of
nutrients that will be available to the growing crop. Therefore, the CAFO regulations specify that
those are required site-specific terms when using the linear approach.
The time of year that manure is applied can influence nitrogen availability because of seasonal
changes in conditions that influence mineralization rates. As a term of the NMP, timing depends
on the specific way in which timing affects nutrient availability in the application rate calculation.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-45

NPDES Permit Writers’ Manual for CAFOs

For example, spring or fall would be sufficient if the nitrogen value for that application is the same
no matter when during the spring or fall manure is applied. On the other hand, the term might be
as specific as “within two weeks before planting” if that is critical to determining the availability
of nitrogen to the growing crop. An operator might prefer to specify the timing of an application
relative to a seasonal time frame for use as a permit term, even if the plan specifies a specific
day or month. (Note that most nutrient management planning software requires identification
of a specific date of application; EPA does not expect that permit terms would dictate a specific
date for manure application). EPA believes that capturing application timing over the course of a
season would be appropriate even if the NMP is more specific, as long as the specific timing is not
critical to determining nutrient availability.
The term method refers to the equipment used (e.g., big gun, injector, sprinkler, broadcast
spreader) to apply the manure. The method of application can affect nutrient availability, the
efficiency of crop use, and the likelihood of nutrient loss from the soil. Surface-applied nutrients
are more likely to be lost with erosion, particularly during heavy rains, if adequate erosion
controls are not in place. Phosphorus loss can also occur in the absence of soil erosion with runoff
of dissolved, soluble phosphorus. Nitrogen loss can also occur in the absence of soil erosion
because of volatilization and/or leaching losses. Fresh or stored manure contains nitrogen in the
form of ammonium, which is subject to loss because it volatilizes as ammonia gas. Incorporation
into the soil reduces volatilization; however, there can be a tradeoff because erosion potential
increases after disturbing the soil surface. Solid manures like feedlot pen manure contain
very little ammonium, making incorporation less critical for conserving nitrogen lost from
volatilization (although still desirable for controlling manure nutrients that can be lost from
runoff and erosion). Nevertheless, incorporation within the root zone increases plant availability
of nutrients. Uniformity of nutrient applications and distance from the root system can also
influence crop response to nutrient applications. Manure and wastewater should also be applied
at rates and with methods that consider and account for all pathways for loss.
The land application method used at a CAFO
often depends on the type of application
equipment available or the method that is most
cost- or time-effective. Many growers choose
to broadcast nutrient application because of
fewer time constraints and lower cost. The
handling system and therefore the form of
manure might also dictate the application
method that is used. For example, solid or
semi-solid materials cannot be effectively
injected into the soil or applied through
an irrigation system, while lagoon liquids
are most economically applied through an
irrigation system.

Land application of manure by injection.
(Photo courtesy of USDA)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

If the rates associated with a method rely on incorporating the manure after a certain number
of days, the number of days should be captured with the method and as part of the timing
requirement because the timing, as it specifically relates to the method of application, will affect
the amount of nitrogen that will volatilize after manure is land applied.
Volatilization coefficients, which correspond with different methods and timing of application,
can be applied to the appropriate nitrogen compounds from the manure analysis where technical
standards account for this type of nitrogen loss. Typical rates are provided in Table 6-6.
Table 6-6. Percentage of nitrogen in applied manure still potentially available to the soil
(ammonia volatilization causes the predicted losses)
Application method

Percentage remaining/delivered

Injection

95%

Sprinkling

75%

Broadcast (fresh solids)

Soil Conditions

Days between application and incorporation:

Warm dry

Warm wet

Cool wet

1

70%

90%

100%

4

60%

80%

95%

7 or more

50%

70%

90%

Source: Table 11-6, USDA-NRCS Agricultural Waste Management Field Handbook,
(after Willrich et al. 1974)

Manure spreading or spraying activities should be planned and managed to prevent nuisances
and an adverse impact on groundwater, surface water, public health, and plants. Degradation
of any aspect of the environment could warrant reevaluation of the use of a selected manure
application system.

Method
CAFOs should always apply manure uniformly and at the approved application rates. Under the
effluent guidelines, CAFOs must record the data (day, month, year) and method of each manure
application. 40 CFR § 412.37(c). Although many equipment options exist, there are basically two
methods of application: subsurface application and surface application. CAFOs must record
weather conditions (e.g., rainfall amounts) at the time of application and for the 24-hour period
before and after application. 40 CFR § 412.37(c)(3). The operator must also periodically inspect
equipment used for land application of manure, litter, or process wastewater. 40 CFR § 412.4(c)(4).
Though the CAFO rules do not specify the frequency of the inspections, EPA recommends
inspections every time the equipment is used. This allows CAFOs to detect and then correct any
potential problems before they cause adverse environmental impacts.
▶ Subsurface Application. Solid, semisolid, and liquid manure can all be applied using
this method. When feasible, this is the preferred method of manure application.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

Equipment Calibration
Once the method of land application is determined, the manure-spreading equipment needs to be
calibrated to ensure that the actual manure application rate matches the planned manure application
rate. Equipment calibration is determining the appropriate setting and speed necessary for a piece of
land application equipment to apply a calculated rate of manure per acre. Calibration helps a producer to
ensure that application at appropriate rates by determining appropriate overlaps, evaluating application
uniformity, monitoring usage and wear and tear in equipment, and determining application settings based
on manure consistency. At a minimum, equipment used to apply manure, litter, or process wastewater
should be calibrated annually.
During calibration, the required or appropriate overlap can be determined. Overlap distances and travel
lane widths are best determined by measuring the distribution of applied material across the spread
pattern. Rain gauges, tarps, or disposable baking pans can be used to collect the applied manure before
it is weighed or measured. Many times, visual estimates of desired overlap can be misleading. Because of
variations in spreader volume and changes in manure moisture content and density, this is especially true
when calibrating litter or solid manure spreaders. Sprinkler overlaps, typically calculated to be the points
where an area is receiving less than half of the average volume across the spread width, generally vary
between 50 to 80 percent, depending on sprinkler type and wind conditions.
Application equipment should be maintained and operated so it applies a given application rate as evenly
as possible across a field. Hot spots or areas of over-application due to operator error, non-calibrated or
worn equipment can increase the occurrence of runoff or ponding, accumulation of nutrients, or excessive
nutrients moving into shallow groundwater. Areas of low application might not produce the realistic yield
that could be achieved on the site, potentially leaving unused nutrients that accumulate or are lost to the
environment.
As equipment is used and becomes older, it loses efficiency, increasing the need for calibration. That is
compounded by the solids, acidity, and salts found in manure, litter, and wastewater that can accumulate
in equipment with use. To monitor system performance, irrigation systems that pump liquids with high
solids or with significant crystal (iron or calcium carbonate/lime) buildup should be calibrated regularly.
Finally, equipment should be calibrated in response
to changes in manure consistency and nutrient
content. When a manure storage structure is
emptied, a higher amount of solids will be removed
and applied to fields than when only wastewater
from the surface of the storage structure is
applied. As the manure density increases, the
equipment should be recalibrated to ensure that
the application rate is within acceptable limits.
Spreaders should also be recalibrated when a
material that is wetter or drier than the litter or
manure spread during the previous calibration
is applied. Different manure sources will require
equipment calibration to account for changes in
nutrient content.

Manure spreader calibration.
(Photo courtesy of USDA/NRCS)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

CAFOs use this method by mechanically incorporating or injecting the manure
into the soil. Mechanical incorporation can be performed using moldboard plows,
chisel plows, or heavy discs. To reduce nutrient losses, CAFOs should incorporate
wastes applied to the land surface before it dries, usually within 2 days of application.
Injection requires a liquid manure spreader and equipment to inject manure below the
soil surface. To prevent nutrient losses, CAFOs should close the openings made by the
injectors following application.

Immediately incorporating manure in the spring will increase the amount of PAN
by reducing ammonia loss. Incorporation in soils with low runoff potential can help
prevent the movement of nutrients and pathogens from animal manure to surface
waters. Where soil erosion is a problem, however, tillage might result in unacceptable
losses of soil and nutrients.

Injection is likely the best method of incorporating liquid and semi-solid animal
manure in reduced-till or no-till cropping systems because crop residues left on the
surface act as a mulch, and the exposed soil surface is minimum.

▶ Surface Application of Liquid Manure (Irrigation). The three predominant systems
used for surface application of liquid animal manure (irrigation) are solid sets, center
pivots, and traveling guns. Solid set systems are a series of sprinklers generally
supplied by underground pipe. Center pivot systems are generally used in large fields
and must be able to travel in a circle. Traveling guns are high-pressure, high-output,
single-nozzle systems that crawl down travel lanes in the field. Liquid wastes can also
be surface applied with tank spreaders.

Irrigation can save considerable amounts of time and labor when applying large
volumes of wastewater or liquid animal manure. Sometimes, CAFOs might need to
dilute animal manure with fresh water for salinity or other plant requirements, or to
facilitate application via irrigation. Irrigation provides flexibility in applying animal
manure during the growing season and has the added advantage of supplying water
during the growing season’s drier periods. Infiltrating liquid can carry much of the
easily volatilized ammonia into the soil, although some ammonia will still be lost from
the spray before it reaches the soil.

The irrigation system should, however, be matched to the topography, cropping
program, nutrient and water needs of the crops, as well as infiltration, percolation rate,
and water holding capacity of the soil. CAFOs should not use irrigation to apply animal
wastes unless solids have been removed or chopped very fine. If solids are present, the
nozzles will clog and the system will not operate properly. Irrigation also can produce
aerosol sprays that can cause odor problems.

▶ Surface Application of Dry, Solid Manure. This application method is very effective
at applying dry, bulky animal wastes such as poultry litter. Box spreaders with a

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-49

NPDES Permit Writers’ Manual for CAFOs

chain‑drag delivery to a fan or spreader mechanism, or tank wagons equipped with
splash plates typically are used for surface applications.

Although this is a relatively easy method for applying animal manure and wastes to the
land, it has several disadvantages. First, when manure is applied to the surface of the
soil without incorporation, most of the unstable, rapidly mineralized, organic nitrogen
from the manure is lost through the volatilization of ammonia gas. Volatilization
increases with time, temperature, wind, and low humidity. Surface application without
incorporation also increases the likelihood of nutrient losses via surface runoff.
Surface runoff losses are more likely on soils with high runoff potential, soils subject to
flooding, soils that are snow-covered or frozen (via runoff once the snow melts or soil
thaws), and soils with little or no vegetative cover. Second, aerosol sprays produced by
mixing manure and air during this type of application can carry odors considerable
distances. Third, this application method provides poor distribution of nutrients,
which can be aggravated by heavy winds. In addition, precision application of manure
and waste, such as poultry litter, with a geared box spreader can be difficult.

CAFOs can reduce nutrient losses when using surface application by implementing
soil conservation practices such as contour strip cropping, crop residue management,
cover crops, diversion terraces, vegetative buffer strips, and grass waterways. More
information about conservation practices is available from the local soil and water
conservation district and USDA’s NRCS.

▶ Irrigation Technologies. Irrigation application systems can be grouped under two
broad system types: gravity flow and pressurized. Gravity-flow systems are particularly
predominant in the arid west. Many irrigation systems rely on gravity to distribute
water across the field. Land treatments (such as soil borders and furrows) are used
to help control lateral water movement and channel water flow down the field. Water
losses are comparatively high under traditional gravity-flow systems due to percolation
losses below the crop-root zone and water runoff at the end of the field.

Pressurized systems—including sprinkler and low-flow irrigation systems—use
pressure to distribute water. Sprinkler system use is highest in the Pacific Northwest,
northern plains, and in eastern states. Center-pivot technology serves as the
foundation for many technological innovations—such as low-pressure center pivot,
linear-move, and low-energy precision application systems—that combine high
application efficiencies with reduced energy and labor requirements. For more
detail on irrigation water management, see ARS’ Irrigation Water Management in
Agricultural Resources and Environmental Indicators at http://www.ers.usda.gov/
publications/ah712/AH7124-6.pdf.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-50

NPDES Permit Writers’ Manual for CAFOs

Gravity-Flow Irrigation
Water is conveyed to the field by means of open ditches, above­ground pipe (including gated pipe)
or underground pipe, and released along the upper end of the field through siphon tubes, ditch
gates, or pipe valves. Such systems are generally designed for irrigation water, and many CAFOs
have not traditionally accounted for the irrigated manure nutrients. Some irrigation systems may
offer nutrient management challenges to CAFOs including: uneven nutrient distribution, flooding
and pooling, excessive volatilization of nitrogen, excessive leaching, and other potential difficulties
in meeting technical standards established in their state.

Timing
Timing of manure application is an important consideration for nutrient availability. The
longer manure nutrients are in the soil before crops take up the nutrients, the more those
nutrients can be lost through volatilization, denitrification, leaching, and surface runoff. CAFOs
should consider the hydrological cycle and hydrological sensitivity of each field when making
management decisions.
▶ Spring Applications. Applications made during this time can conserve nutrients if
nutrients are applied in coordination with plant crop needs because it is just before
the period of maximum crop uptake, allowing for more efficient nutrient utilization.
In these cases the threat of surface runoff and leaching can be diminished. However,
nutrients added in early spring can also be quite vulnerable to loss. Increased
precipitation, snow melts, and warming soils contribute to saturated soils that can
result in high nutrient loss unless applications are timed appropriately with crop
nutrient uptake.
▶ Summer Applications. Early summer is a good time to apply manure because it is
generally the time of maximum crop uptake. One consideration is that improper
manure application rates and methods can damage growing crops. Options for
applying manure in the early summer include side-dressing manure by injecting
it between row crops, irrigating liquid manure over corn rows when the corn is 3 to
12 inches tall (taller corn stalks can suffer more leaf damage), or applying manure
to forages such as hay fields and grasses after the first and second cuttings or to
pastures with small stubble. CAFOs can also apply nutrients to harvested stubble
fields in mid- to late-summer. Nitrogen in the manure stimulates more growth of
cover crops, especially non-legume species that require nitrogen. The cover crop
takes up the nutrients and holds them in an organic form in the plant, preventing
them from leaching or being tied up in the soil complex. The nutrients are then more
available for subsequent years’ crops when the crop residue breaks down.
▶ Fall Applications. Fall application of manure generally results in greater nutrient
losses, especially if manure is applied to a soil without any vegetative cover.
Increased nutrient losses occur because mobile nutrients such as nitrogen leaching
out of the soil. Many of the non-leachable nutrients react with the soil to form
insoluble compounds that build soil fertility, but some are bound so tightly that they
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-51

NPDES Permit Writers’ Manual for CAFOs

might not be available for the next crop. In fall, manure is best applied at low rates
to fields that will be planted in winter grains or cover crops. If winter crops are not
planted, CAFOs should apply manure to the fields containing the most vegetation or
crop residues. Sod fields to be plowed the next spring are also acceptable, but fields
where corn silage is removed and a cover crop not planted are undesirable sites.
▶ Winter Applications. The greatest nutrient losses typically occur with winter manure
applications to frozen, snow-covered, or saturated soils. Research indicates that win­
ter applications increase pollutants in runoff during spring thaw and rainfall events.
Most of the seasonal runoff occurs during snowmelt in late winter or early spring.
Manure applied in winter generally does not have the opportunity to dry and anchor
to the soil surface or to be incorporated into the soil. CAFOs that apply manure dur­
ing the winter must do so in compliance with the state’s technical standards unless
winter application is prohibited by the state technical standards. Such protocols must
account for the form of material that would be applied (e.g., liquid, semi-solid, or dry
manure). In addition, such standards should address the time at which the materials
would be applied relative to periods when runoff could occur, the fraction of precipita­
tion that runs off the land in meltwater and in response to winter rains (as affected, in
part, whether the soil is frozen or not), the time it takes runoff to travel to waters of the
U.S. (as affect by slope, distance to waters, roughness of the land surface, and whether
runoff is in contact with the land surface), and other relevant factors, as appropriate.
Nutrient applications should be managed in a way that accounts for the right amount, the right
source (manure/fertilizer), the right placement, and most important the right timing. While
different seasons can be more or less favorable for crop nutrient utilization, the right timing
should ultimately be coordinated with planted crop needs for efficient nutrient utilization and
to minimize nutrient loss. CAFOs should check their state regulations to determine whether fall
or winter land application is allowed. Manure, litter, and wastewater storage structures should
include adequate capacity to store materials that accumulate during those times when, under the
technical standards for nutrient management, land application would be prohibited.

The Maximum Amount of Nitrogen and Phosphorus from Manure,
Litter and Process Wastewater
For the linear approach, the enforceable term for the land application rate is the maximum amount
of nitrogen and phosphorus from manure, litter, and process wastewater in pounds per acre, per
year, in chemical forms determined to acceptable to the Director. 40 CFR § 122.42(e)(5)(i)(A). That
value does not include residual nutrient credits or nutrients available from other sources because
under the linear approach, the nutrients from those sources are already accounted for as separate
permit terms. The maximum application rate must be calculated for each crop on each field to be
used for land application for each year of permit coverage.
The purpose of the term, outcome of the field-specific risk assessment (in both the linear and
narrative rate approaches) is to determine the appropriate limiting nutrient for developing
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-52

NPDES Permit Writers’ Manual for CAFOs

land application rates (i.e., whether phosphorus or nitrogen limits the amount of manure,
litter, or process wastewater that can be applied or whether land application is to be avoided
altogether). Therefore, the field-specific risk assessment plays an important role in determining
the appropriate amount of both nitrogen and phosphorus to apply. Therefore, what constitutes the
term, maximum amount of nitrogen and phosphorus from manure, litter, and process wastewater,
depends on the term outcome of the field-specific risk assessment. Section 6.5.1 describes two
methods for writing the permit term, outcome of the field-specific risk assessment, when the
assessment tool is a phosphorus site index. The first method, the multiple risk level, lends itself to
the linear approach.
The maximum amount of nitrogen from manure, litter, and process wastewater is the maximum
amount of nitrogen from manure that can be applied to a field for the specified crop. The amount
is calculated on the basis of the terms for the total nitrogen recommendation minus the nitrogen
credits and any other additions of PAN. The amount must also account for the form, source,
method, and timing of application, all of which are terms under the linear approach. Where
the risk assessment allows nitrogen-based application, the maximum amount of nitrogen from
manure should supply the difference between the crop’s nitrogen fertilizer recommendation (or
for legumes, the crop nitrogen removal or other state-specific nitrogen recommendation) and
other sources of PAN.
The maximum amount of phosphorus from manure, litter, and process wastewater will be
determined for every crop according to each year’s field risk rating. The maximum amount of
phosphorus from manure, litter, or process wastewater can be calculated as the quantitative value
for the allowable application rate determined for a field by
the field-specific risk assessment. The maximum amount of
phosphorus from manure, litter, or process wastewater needs
to be reported only for years where land application is limited
to a phosphorus-based rate. For example, assuming that the
operator is only using manure as a nutrient source, if the fieldspecific risk assessment determines that manure application
should be limited to the annual crop phosphorus removal
rate in year 1, the crop removal rate will define the value that
constitutes the term maximum amount of phosphorus from
manure, litter, or process wastewater. If in the second year the
risk is reduced so that manure could be applied at an nitrogenbased rate, the maximum amount of phosphorus from manure
that could be applied could be reported as nitrogen-based
without quantitatively defining the phosphorus limit. For every
field, there will be an individual nitrogen and phosphorus limit
for every crop that is based on the crop(s) planned to be grown
each year in the NMP and that year’s risk assessment outcome.

Hog manure sampling for nutrient
analysis. (Photo courtesy of USDA/NRCS)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.2. Additional Site-Specific Terms: Linear Approach

6-53

NPDES Permit Writers’ Manual for CAFOs

The Methodology to Account for the Amount of Nitrogen and
Phosphorus in the Manure to be Applied
Permitted CAFOs must calculate the maximum amount of manure to be land applied at least once
each year on the basis of the results of the manure nutrient analysis. 40 CFR §§ 122.42(e)(5)(i)(A),
(ii)(D). The tons or gallons of manure to be applied are not the enforceable permit term. The
enforceable term is the maximum number of pounds of nitrogen and phosphorus from the manure
to be applied. The operator is held to that rate when calculating the tons or gallons of manure to
be land applied. Although the rate constitutes a numeric limit in the permit, the operator may
apply fewer nutrients from manure but may not exceed the maximum amount of nitrogen and
phosphorus from manure, litter, and process wastewater that is established as a term of the NMP.
Under the linear approach, the methodology that is used to account for the amount of nitrogen
and phosphorus in the manure that is to be applied is a permit term. 40 CFR § 122.42(e)(5)(i)(A).
As mentioned above, operators of permitted Large CAFOs must calculate the actual amount
of manure to be applied annually to supply the calculated amount of nutrients to be applied
from manure. The amount of nitrogen and phosphorus in the calculated amount of manure can
be determined with the use of the manure test results. For more on how to read and interpret
a manure analysis, see Chapter 5.9.1. Large CAFOs must use the results of the most recent
representative manure tests for nitrogen and phosphorus taken within at least 12 months of the
date of land application. Medium and Small CAFOs must apply manure consistent with BPJ-based
requirements established in the permit for accounting for the nutrient content of the manure.
The NMP must describe the calculations that will be used to translate the pounds of nitrogen and
phosphorus to be applied into an application rate for manure, litter, or process wastewater.

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach
The narrative rate approach allows rates of nutrient application from manure to be expressed in a
narrative as long as it includes the maximum amount of nitrogen and phosphorus derived from all
sources. The six site-specific terms described in Section 6.5.1 must be terms of the permit when using
either the linear or narrative rate approach for expressing land application rates in NMPs. They are
▶ The fields available for land application.
▶ Timing limitations for land application.
▶ Outcome of the field-specific risk assessment.
▶ Planned crops or other use.
▶ Realistic crop yield goals.
▶ Total nitrogen and phosphorus recommendation for each crop.
In addition to those six permit term requirements, three additional site-specific permit term
requirements apply only to the narrative rate approach.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach

6-54

NPDES Permit Writers’ Manual for CAFOs

▶ The maximum amount of nitrogen and phosphorus from all sources.
▶ Alternative crops.
▶ The methodology used to derive the actual amount of manure that is applied.

The Maximum Amounts of Nitrogen and Phosphorus from All
Sources
Unlike the linear approach, where land application rates are expressed in terms of the amount
of nutrients to be applied from manure, the narrative rate approach sets an upper limit on the
amount of nutrients to be applied from all sources. The term is the maximum amounts of nitrogen
and phosphorus derived from all sources of nutrients for each crop identified in the NMP in
chemical forms determined to be acceptable to the Director, in pounds per acre, for each field.
40 CFR § 122.42(e)(5)(ii)(A). An additional distinction between the maximum limits required by
the linear and narrative rate approach is that in the linear approach, the maximum limit must
be identified for each year manure is applied; in the narrative rate approach, the maximum limit
is identified only for each crop but does not need to be reported each year that crop is planted.
40 CFR §§ 122.42(e)(5)(i) and (5)(ii).
The outcome of field-specific risk assessment is used to determine the appropriate limiting nutrient
for developing land application rates (i.e., whether phosphorus or nitrogen limits the amount
of manure, litter, or process wastewater that can be applied or whether land application is to
be avoided altogether). However, in the narrative rate approach, the term maximum amount of
nitrogen and phosphorus from all sources should not be exclusively dependent on the outcome
of the field-specific risk assessment for the potential for nitrogen and phosphorus transport as the
maximum limit was described for the linear approach.
The maximum amount of nitrogen from all sources under the narrative rate approach is based on
the maximum amount of nitrogen that can be applied to a field for the specified crop based on
crop type, yield goal, and current soil test (where states rely on nitrogen soil testing). That is the
crop’s fertilizer recommendation or for legumes, the crop nitrogen removal rate, or other statespecific nitrogen limit for legumes. That value is the same value that is reported for the term, total
crop nitrogen recommendation.
To preserve the flexibility of the narrative rate approach, the maximum amount of phosphorus
from all sources can be set for each crop according to the maximum amount of phosphorus
applied in any one year for any one crop as dictated by the outcome of the field-specific risk
assessment. For example, the maximum amount of phosphorus from all sources applied in one
given year may be the amount of phosphorus in an nitrogen-based application.
The same crop may be planted more than once over the course of a 5-year NMP. Each time the
crop is planted it can receive different amounts of nitrogen and phosphorus (i.e., a legume may
or may not have manure applied to it. A maximum amount of nitrogen and phosphorus from all

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach

6-55

NPDES Permit Writers’ Manual for CAFOs

sources does not need to be identified each time the crop is planted and associated with a specific
crop year. This is illustrated in the following example.
The NMP illustrated in Figure 6-9 shows a corn-soybean rotation with varying rates of manure
application and a risk that varies with each crop and management of that crop. As discussed in
Section 6.5.1 under the subsection Additional Considerations for Implementing the Outcome of the
Field-Specific Risk Assessment when Utilizing a Phosphorus Site Index, planned rates of application
should not exceed the recommended rates identified by the phosphorus site index. Given that the
risk fluctuates with different crops and years, different rates of manure are applied that follow the
P-Index recommended rates. Therefore, in year 1, an nitrogen-based rate is applied to corn but
in year 3, because the risk increases, manure is applied at the crop phosphorus removal rate as
recommended by this state-specific P-Index. More phosphorus is applied in an nitrogen-based
rate than in a rate that supplies the crop phosphorus removal; therefore, the maximum amount of
phosphorus that is applied to a corn crop in this NMP is the amount applied under the nitrogenbased rate. The soybean crop is planted twice in this NMP. In the second year, manure is applied
at the soybean phosphorus removal rate and in year 4, no phosphorus is applied. Therefore, the
maximum amount of phosphorus applied to soybeans is the soybean phosphorus removal rate.
The field-specific assessment plays an important role in determining the appropriate amount of
both nitrogen and phosphorus to apply each year and can result in different amounts of nutrients
applied each time the same crop is
planted. Disassociating the amount
recommended by the risk assessment
from a specific crop-year in the NMP
allows flexibility to change the crop
rotation or the crops grown as intended
under the narrative rate approach. In
addition to changing the sequence
that crops are planted, the narrative
rate approach also allows a change
in actual crops grown as long as the
nitrogen and phosphorus application
rates are calculated in accordance with
the approved methodology (see the
section below on alternative crops).
Permitted CAFOs must comply with all
limits and conditions of their permits.
That includes the outcome of the fieldspecific risk assessment. Therefore,
manure and other nutrient sources
can be applied up to the identified
maximum amount of nitrogen and

Figure 6-9. An illustration of a 5-year NMP for a corn-soybean rotation.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

phosphorus from all sources limits identified in the permit so long as the field risk rating is
maintained as well as all other established permit limits and conditions (For ways in which
application rates can be changed without incurring a substantial permit modification, see Section
6.5.1 under the subsection Additional Considerations for Implementing the Outcome of the FieldSpecific Risk Assessment when Utilizing a Phosphorus Site Index and Section 6.5.4).

Alternative Crops
A key difference between the linear and narrative rate approaches that allows for greater flexi­
bility under the narrative rate approach, is that the narrative rate approach allows the NMP to
include alternative crops that may be planted in lieu of those included in the planned rotation. If
alternative crops are included, the NMP must also identify for each alternative crop realistic yield
goals and nitrogen and phosphorus recommendations from sources specified by the Director. The
term alternative crops includes the alternative crops listed in the NMP, along with their associated
yield goals and nitrogen and phosphorus recommendations. 40 CFR § 122.42(e)(5)(ii)(B).
If an alternative crop is used, the maximum amounts of nitrogen and phosphorus from all sources
and the amount of manure to be applied must be determined in accordance with the methodology
that is included as an enforceable permit term (as discussed below). The terms and factors
associated with alternative crops would be the same as the terms and factors required for the crops
included in the planned rotation in the NMP.
It is important to recognize that any increase in an outcome of the field-specific risk assessment
that results from incorporating an alternative crop into the planned crop rotation will still be
considered a substantial change to the plan. 40 CFR § 122.42(e)(6)(iii)(D). The amount and timing
of nutrients to be applied is likely to change with a change in the planned crop rotation. As
discussed in Section 6.5.1, this type of change could affect the outcome of the field-specific risk
assessment for an individual crop year. A CAFO operator must ensure that there is no increase the
outcome of the field-specific risk assessment when
implementing an alternative crop; otherwise,
the operator must follow the substantial change
procedures for revising a plan.

Sunflower crop. (Photo courtesy of USDA/ARS)

It is also important to recognize that when
alternative crops are used, application rates
might need to be adjusted for all years after
implementing the alternative crop. That is
especially important if a legume crop is added
or removed from a rotation because of the
change in PAN credits that are accounted for
in the methodology. Additionally, if a manure
application rate is adjusted because of an
alternative crop, mineralization credits for

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

future years could also change. Those changes are accommodated by the flexibility allowed to
an operator when using the narrative rate approach and would not be considered substantial
changes.

The Methodology by which the NMP Calculates the Amount of
Manure to be Land Applied
Rates of application that are expressed using either the linear and narrative rate approach
must include the methodology for calculating the amount of manure to be land applied;
that methodology is captured as an enforceable term. 40 CFR §§ 122.42(e)(5)(i)(A), (ii)(A).
Under, the narrative rate approach, the methodology must account for the following factors
part 122.42(e)(5)(ii)(A):
▶ Credits for PAN in the field.
▶ The amount of nitrogen and phosphorus in the
manure to be applied.
▶ Consideration of multi-year phosphorus
application.
▶ Accounting for all other additions of plant
available nitrogen and phosphorus to the field.
▶ Form and source of manure, litter, and process
wastewater.
A Global Positioning Satellite (GPS) navigation
system facilitates accurate planting, fertilization,
and harvesting. (Photo courtesy of USDA/FSA)

▶ Timing and method of land application.
▶ Soil test results.
▶ Volatilization of nitrogen and mineralization of
organic nitrogen.

The factors listed above are not themselves considered permit terms, but the methodology used
to account for them in the CAFO’s permit is a term. Thus, the CAFO operator will be bound by the
methodology and the way in which the above factors are accounted for in calculating the rates of
manure application. As long as the methodology prescribed in the NMP is followed and includes
all the listed factors, the calculated amount of manure, litter, or process wastewater can change
from year to year.
The first six factors listed above are terms under the linear approach. 40 CFR § 122.42(e)(5)(i)(A).
Regardless of whether they are expressed as permit terms under the linear approach or as factors
of the methodology under the narrative rate approach, the information is typically used in the
same manner when calculating rates of manure application. Therefore, the discussions of these
terms under the linear approach (see the discussion above in Section 6.5.2) also apply here,
and the factors are not further discussed in this section. The difference is that, unlike the linear
approach, where the factors are terms, the narrative rate approach allows flexibility for the factors
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

to fluctuate from year to year without notifying the Director. As described in Chapter 4.2.3, some
of this information must be included in the annual report for CAFOs that use the narrative rate
approach to assure the permitting authority and the public that the CAFO is operating within the
limits established by the permit given the flexibility of the narrative rate approach permit terms.
40 CFR § 122.42(e)(4).

Results of the Soil Test
The annual calculation of the amount of manure to be applied must account for the results of
the most recent soil test conducted in accordance with sampling requirements approved by the
Director. Soil sampling requirements should be included in the technical standards for nutrient
management. The ELGs specify that Large CAFOs subject to subparts C and D must test their soil
for phosphorus at least once every 5 years. Some states’ technical standards require sampling
to be done more frequently (e.g., annually or 2 to 3 years). Some states require more frequent
sampling on fields that have reached higher soil test phosphorus levels. The annual calculation
of the amount of manure to be applied must rely on the results of the most recent soil test; even
if sampling is conducted more frequently than required by the Director. If a soil test is taken
only once over the course of a 5-year permit term, the amount of plant available soil phosphorus
indicated by that analysis is assumed on an annual basis. Some states may also require testing for
soil nitrogen. The methodology for calculating the amount of manure to be land applied should
take that into account.
How the soil test is factored into the methodology under the narrative rate approach may differ
from state to state. Soil tests should be included as a variable in the field risk assessment method.
Different assessments use the soil test differently. The examples of assessment methods provided
in Section 6.5.1 show that some states use soil test thresholds while others rely on a P-Index. Soil
test thresholds directly rely on the soil test value to determine if manure nutrients should be
applied at an nitrogen-based rate, phosphorus-based rate, or not applied at all while P-Indices
use the soil test along with many other variables to make that determination. Each state has the
flexibility to determine which assessment method it uses and how that assessment incorporates
the soil test results.
When states require a soil test to be taken more frequently than once over the course of a 5-year
permit cycle, the CAFO operator should recalculate the field-specific risk assessment so that
the outcome is based on the result of the most recent test. If soil test levels for phosphorus are
increasing, the potential for phosphorus to be transported from a field could be increasing as
well. The CAFO operator should be aware of such a change so that changes in manure application
rates or conservation practices can be implemented and updated in the NMP to minimize losses
and maintain the risk rating captured as a term for that field. EPA encourages frequent soil testing
and reevaluation of the field risk assessment for all CAFO operators, regardless whether they are
using the linear or narrative rate approach. The CAFO operator should always be aware of the
current field conditions to ensure the minimization of nutrient transport from each field using
the most recent data.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Mineralization of Organic Nitrogen and Volatilization of Nitrogen
As with the linear approach, the narrative rate approach must rely on and incorporate the
results of the most recent representative manure tests taken within 12 months of the date of land
application when calculating the rates of application.
The amount of manure to be land applied is determined on the basis of the amount of plant
available nutrients in the manure. A manure analysis provides the amount of nitrogen (typically
as total nitrogen, ammonium and phosphorus) contained in the manure samples that were
submitted (see Chapter 5). The manure analysis is used to determine the amount of PAN.
PAN is determined by accounting for both nitrogen losses (volatilization) and nitrogen gains
(mineralization). State technical standards for nutrient management should identify appropriate
volatilization and mineralization rates; those rates are a part of the methodology under the
narrative rate approach to ensure proper calculation of appropriate manure application rates.
Losses of nitrogen from volatilization vary depending on the form, source, timing and method
of application. Gains of PAN as a result of mineralization will vary depending on the timing of
application and the type of manure that is being used (e.g., dairy, beef, poultry, or swine). Some
organic nitrogen will be available the year it is applied, and some will become available in the
years following a land application event. Approximately 50 to 75 percent of the total nutrients
applied are likely to be plant available during the first year. Nitrogen not used by the crop(s)
planted following an application is available for subsequent crops or they are subject to loss by
erosion or leaching. It is therefore important to time manure applications to coincide with peak
nutrient uptake by the crop.
The volatilization and mineralization rates identified by the state technical standards must be
applied to the appropriate manure nitrogen fractions to determine the amount of PAN, supplied
from the manure to be added to a field for a crop. In general, volatilization factors are applied
to the ammonium result from the manure
analysis. Mineralization factors are applied
to the organic nitrogen results. If the manure
analysis provides only total nitrogen and
ammonium, the amount of organic nitrogen
can be determined as the difference between
the two (total N – NH4+).
In practice, the narrative rate approach (and
the linear approach) will require that amounts
of manure to be land applied be translated
from pounds of nutrients into tons or gallons
of manure to be applied. The information
presented to the public in the CAFO’s NMP
will include the projected tons or gallons
of manure for the planned crop rotation for

Land application of manure by a honeywagon.
(Photo courtesy of USDA/NRCS)

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Applying volatilization and mineralization
factors to the annual manure analysis
results will provide an adequate estimate for
calculating the tons or gallons of manure
to be applied to supply the appropriate
amount of nitrogen to the crop. While
this estimate is generally adequate, the
volatilization and mineralization coefficients
that are the basis for those values include
certain assumptions about environmental
conditions that affect the processes; actual
conditions, and therefore actual volatilization
and mineralization rates, could differ from
those estimated.
Plant tissue testing and pre-sidedress
nitrate testing might be effective tools
for more accurately determining nitrogen
deficiencies (and the need for supplemental
nitrogen application) and for determining
excess nitrogen. Plant tissue tests and presidedress nitrate tests are typically taken
after a portion of the manure or fertilizer
applications have been made on a field. The
tests should be used to adjust the amount
of additional manure or fertilizer that needs
to be applied to meet the crop needs.
A CAFO’s NMP may include plant tissue
testing as part of the CAFO’s methodology
as long as it is done consistently with state
technical standards.

each field. That provides the permitting authority and the
public an opportunity to review, before permit issuance,
the adequacy of the CAFO’s methodology. Additionally,
the permitting authority and public can review the way the
CAFO uses the methodology to calculate the appropriate
amount of manure to be applied. Again, the planned crop
rotations and projected amounts are not terms, because
they will need to be recalculated each year on the basis of
updated information; however, the projections will allow
the public to see how the methodology (which is a term) is
applied to a projected set of facts to calculate the amounts
to be land applied.
The narrative rate approach provides additional flexibility.
In addition to addressing changes in the management of
the operations, CAFOs can adjust their rates of application
because of fluctuations in any of the factors addressed by
the narrative rate methodology. For example, if the NMP
projects an amount of manure to be applied according to
incorporation of solid manure, the operator could instead
apply process wastewater from a lagoon. Form, source,
and method of application are all factors affected when
an operation makes that type of change. Factors of the
methodology can change and possibly result in a change
to the projected tons of manure to be applied to gallons of
wastewater to be land applied. The flexibility is allowed by
the narrative rate because the new amount of manure to
be applied will be predictably and accurately calculated
according to the required methodology.

If an NMP is developed by hand or using software
that either is not documented publicly or has not been
determined to satisfy all the factors in accordance with the state’s technical standard, the
methodology must be documented in the NMP itself. The methodology may; however, be
embedded in a software program if the permitting authority determines that the program
adequately accounts for the required factors in accordance with the state’s technical standards.
In addition, documentation that fully expresses how the software accounts for each of the
listed factors must be available to the Director and to the public to satisfy the public review
requirements of the CAFO rule. Section 6.6 should serve as guidance for permitting authorities as
to what EPA expects in nutrient management planning programs to ensure that it encompasses
all the factors of the methodology listed above.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.5.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

6.5.4. Substantial Changes
The outcome of the field-specific risk assessment and the maximum amount of nitrogen and
phosphorus from all sources or the maximum amount of nitrogen and phosphorus from manure,
litter, or process wastewater are site specific permit terms. Changes to these terms (any increase
to the outcome of the field-specific risk assessment and any change to the maximum amount
of nitrogen and phosphorus) are considered substantial changes that trigger a permit change.
40 CFR § 122.42(e)(6)(iii)(B). Given the relationship between the amount of nutrients to be applied
and the field-specific risk assessment, it is necessary for CAFOs to recalculate the outcome of fieldspecific risk assessment when there are changes to any variables that are used in calculating the
outcome of the field-specific risk assessment. That becomes more apparent when the field-specific
risk assessment is a P-Index because of the numerous variables used by that tool for determining
risk. Because a P-Index often includes the manure application rate as one of the variables; this
would include changes to the planned rate of manure application, even if the new planned rate
does not exceed the maximum limit identified in the permit. Figure 6-10, below illustrates when
a phosphorus site index would need be recalculated when NMP implementation deviates from
what was planned when the NMP was first developed.

Figure 6-10.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application
6.5.4. Substantial Changes

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

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NPDES Permit Writers’ Manual for CAFOs

The permit term for the outcome of the field-specific risk assessment can be written in various
ways. Two have been discussed in this Manual. The process illustrated in Figure 6-10 is applicable
regardless of how the permit term for the outcome of the field-specific risk assessment is written.
When a single overall risk for a field is used (the highest risk), only changes that result in an
exceedance of that risk are substantial. When multiple risks are used for a field (typically
associated with each crop year) any change that results in an exceedance of any one risk over the
course of the NMP is substantial.
The CAFO operator is responsible for ensuring that any changes in management that deviate
from what was proposed in the submitted NMP do not increase the field risk rating beyond the
rating included as a term in the permit. If an operator’s NMP plans for the land application of
nutrients at rates below the limits established by the permit term maximum amount of nitrogen
and phosphorus from all sources (e.g., planned application of manure at the crop phosphorus
removal rate when the risk assessment allows for an nitrogen-based rate), the operator can choose
to apply at rates that are higher than planned without violating the permit, as long as the rates do
not exceed the maximum amount of nitrogen and phosphorus from all sources (or from manure,
litter, and process wastewater under the linear approach) and as long as the increased application
rate does not increase the field risk beyond that allowed by the permit term outcome of the fieldspecific risk assessment.

6.6. Permit Terms for Land Application Protocols Using
a Sample NMP
This section uses a sample NMP (Appendix P, Sample Nutrient Management Plan) to identify
example permit terms under each approach. Because many permit terms are based on the
technical standard for nutrient management, a sample technical standard is also provided
with the sample permit (Appendix O, Sample Site-Specific NPDES General Permit). The sample
technical standard that is attached to the sample permit was developed by EPA for illustrative
purposes only and is not a state Director-identified and approved technical standard for any state.
The permit writer needs to be familiar with the state’s technical standards to properly determine
that permit terms based on information in a CAFO’s NMP are developed in accordance with the
state’s requirements. To help illustrate the importance and relationship that technical standards
play in developing permit terms, a reference to the sample technical standard is given for the
example, where appropriate. Additionally, for each term, the location in the plan is identified.
While the NMP contains 16 fields and is developed for 5 years, permit terms are not illustrated for
each field for all 5 years because many of the terms are identical and the information is repetitive.
As described above, this section provides guidance to permitting authorities on EPA’s expecta­
tions as to what needs to be addressed by automated nutrient management planning tools to
ensure that they encompass all the terms and factors required by the CAFO rule. The sample
plan referenced in this section was developed using Manure Management Planner (MMP).
EPA recognizes that many states use different programs, which may encompass all of what
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6-63

NPDES Permit Writers’ Manual for CAFOs

is described below. Data may be contained in program files and not explicitly provided to an
operator as not all the information is necessary to an operator in the day-to-day management of
his operation. No matter how the data are stored or displayed, to obtain permit coverage, it is the
CAFO’s responsibility to ensure that the information is provided to the permit writer.
The sections below follow the order of the discussion of site-specific permit terms for land applica­
tion protocols in Section 6.5. For each of the terms identified in the CAFO rule, Section 6.6 identi­
fies the site-specific information from the sample NMP that would be captured as permit terms.

6.6.1. Site-Specific Terms: Linear and Narrative Rate
Approaches
Fields Available for Land Application
Data sources:
1. Sample NMP: Table 6.1 Field Information and Field Maps
2. Technical Standards reference: Appendix A9 of the Iowa DNR, Manure Management Plan
Form, 65.17(16) - Soil sampling requirements for fields where the P-Index must be used
Example term:
Field ID

Subfield ID

Total spreadable acres

Bob’s Farm-North

8N

56.4

Bob’s Farm-South

8S

79.6

A note on using the sample NMP and technical standard to develop the permit term:
As discussed in Chapter 6.5.1, technical standards may limit the allowable size of a field by setting
limits on the acres that a soil sample can represent. This sample technical standard does not
prohibit grouping soil test results from soil samples. Therefore, field acres represented by similar
analyses have been grouped in the sample NMP.

Timing Limitations for Land Application
Data sources:
1. Sample NMP:
• Table 6.1 Field Information and Field Maps
▷ for field slopes
• Table 6.6 Manure Application Planning Calendar
▷ for timing restrictions
2. State Technical Standard reference: State NRCS Conservation Code 590 (December 2008).

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

Text from the state-specific NRCS code 590:
Nutrients and organic nutrient sources shall not be surface applied to frozen, snow
covered ground, or saturated soil if a potential risk for runoff exists. A potential risk for
runoff exists on slopes greater than 5% unless erosion is controlled to soil loss tolerance
levels (T) or less. Manure may be surface applied to frozen, snow covered or saturated
ground if a potential risk for runoff exists only under one of the following conditions.
• Where manure storage capacity is insufficient and failure to surface apply creates a
risk of an uncontrolled release of manure.
• On an emergency basis.

Example term:
Field ID

Subfield ID

Year

8S

2010

Bob’s Farm South

2011
2012
2013
2014

Limitations
The slope is 7%, therefore:
Manure may only be surface applied to this field
when the ground is frozen, snow covered or
saturated if one of the following conditions exists:
1. Where manure storage capacity is insufficient
and failure to surface apply creates a risk of an
uncontrolled release of manure
2. On an emergency basis

In contrast, an example of a field with a slope of less than 5 percent, the term could be illustrated as
Example term:
Field ID

Subfield ID

Year

Sample-1

2010

Sample

2011

Limitations
The slope is 3.5%, therefore:
No limitations. Manure may be applied year round.

2012
2013
2014

A note on using the sample NMP and technical standard to develop the permit term:
Although in emergency situations, the sample technical standards allow for application to occur
on frozen, snow covered, and saturated ground, EPA encourages that no application occur by
any method to any ground that is frozen, snow covered, or saturated. EPA points out that while a
standard may allow for that type of application to occur, the plan writer may choose that it is not the
best management practice and write a more protective limit into the permit.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

Outcome of the Assessment of the Potential for Nutrient and
Phosphorus Transport for Each Field
Data source:
1. Sample NMP: Table 5.3, Nitrogen and Phosphorus Risk Analysis—Iowa Phosphorus Index
2. Technical Standard:
• Appendix A9 of the Iowa DNR, Manure Management Plan Form,
Chapter 567—65.17(17)
Example term when using multiple risks for a field that are based on each crop year’s risk
Field ID
Bob’s Farm South

Subfield ID

Year

P loss
risk

8S

2010

Low

2011

Medium

Manure shall not be applied in excess of two times the
crop phosphorus removed with crop harvest over the
period of the crop rotation.

2012

Medium

Manure shall not be applied in excess of two times the
crop phosphorus removed with crop harvest over the
period of the crop rotation.

2013

Medium

Manure shall not be applied in excess of two times the
crop phosphorus removed with crop harvest over the
period of the crop rotation.

2014

Medium

Manure shall not be applied in excess of two times the
crop phosphorus removed with crop harvest over the
period of the crop rotation.

Allowable manure application rate
Manure shall not be applied in excess of the nitrogen
needs of the crop.

Or
Example term when using a single risk outcome for a field based on the highest risk for all
crop years
Field ID
Bob’s Farm South

Subfield ID

P loss
risk

8S

Medium

Allowable manure application rate
Manure shall not be applied in excess of two times the crop
phosphorus removed with crop harvest over the period of the
crop rotation.

A note on using the sample NMP and technical standard to develop the permit term:
The allowable manure application rate associated with each risk level is not provided in the NMP
output Table 5.3. The allowable manure application rate basis was pulled from the state technical
standards [Appendix A9 of the Iowa DNR, Manure Management Plan Form, Chapter 567—
65.17(17)] to develop the complete and appropriate permit term.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

Planned Crops or Other Use (Fallow, Pasture, etc.) for Each Field
and Each Year
Data source:
1. Sample NMP: Table 6.5, Planned Crops and Fertilizer Recommendation
2. Technical Standard reference: Not applicable
Example term:
Field ID

Subfield ID

Year

Crop

8S

2010

Soybean

2011

Corn

2012

Soybean

2013

Corn

2014

Soybean

Bob’s Farm South

Realistic Annual Crop Yield Goal for Each Field
Data sources:
1. Sample NMP: Table 6.5, Planned Crops and Fertilizer Recommendation
2. Technical Standard Reference: Appendix A9 of the Iowa DNR, Manure Management Plan
Form, Chapter 567—65.17(6) - Optimum crop yield and crop schedule.
Example term:
Field ID

Subfield ID

Year

Crop

Yield goal

Units

8S

2010

Soybean

61

bu/acre

2011

Corn

195

bu/acre

2012

Soybean

61

bu/acre

2013

Corn

195

bu/acre

2014

Soybean

61

bu/acre

Bob’s Farm South

A note on using the sample NMP and technical standard to develop the permit term:
According to Appendix A9 of the Iowa DNR, Manure Management Plan Form, Chapter 567—
65.17(6) - Optimum crop yield and crop schedule, optimum crop yield goals could have determined
in accordance with one of the following methods:
▶ Soil Survey Interpretation Record
▶ USDA county crop yields
▶ Proven Yield Methods
In this case, USDA county crop yields were used. Appendix A8 of the Iowa DNR, Manure Manage­
ment Plan Form, contains Agriculture Statistics on County Corn and Soybean Yield Averages.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

Total Nitrogen and Phosphorus Recommendations for Each Crop by
Field and Year
Data sources
1. Sample NMP: Table 6.5, Planned Crops and Fertilizer Recommendations
•

Provides fertilizer recommendations and removal rates

2. Technical Standard References:
•

Appendix A5 of the Iowa DNR, Manure Management Plan Form, Crop Nitrogen
Usage Rates Factors for Various Crops

•

Appendix A6 of the Iowa DNR, Manure Management Plan Form, Nutrient Removal
for Iowa Crops

•

IA NRCS 590 conservation code (December 2008), Manure and Organic By-Product
Nutrient Application Rates, Section A. Nitrogen Application
° Manure application to legumes

Example term:
Field ID
Bob’s Farm South

Subfield ID

Year

Crop

Total N

Total P2O5

8S

2010

Soybean

232 lbs/A

49 lbs/A

2011

Corn

210 lbs/A

73 lbs/A

2012

Soybean

232 lbs/A

49 lbs/A

2013

Corn

210 lbs/A

73 lbs/A

2014

Soybean

232 lbs/A

49 lbs/A

A note on using the sample NMP and technical standard to develop the permit term:
In Table 6.5 of the sample NMP, the crop nitrogen recommendation for legumes is zero. However,
the IA NRCS 590 conservation code (December 2008) allows for manure or other organic byproducts may be applied on legumes at rates equal to the estimated removal of nitrogen in the
harvested portion of the crop that is removed from the field in that growing season. Therefore, the
permit term for nitrogen for soybeans is reported according to the removal rate of 3.8 lbs N/bu of
soybean harvested and the yield goal. In addition to being reported in the NMP, it is provided in
Appendix A6 of the Iowa DNR, Manure Management Plan Form.
The nitrogen recommendation as reported in MMP in Table 6.5 of the sample NMP indicates that
corn, following soybeans has a recommendation of only 160 lbs/acre. That is 50 lbs less than the
typical, 210 lbs/acre recommendation for corn (based on the recommendation for a corn crop
following a corn crop. This rotation with this recommendation is not shown in the simplified NMP
of Appendix P). The recommendation is lowered to account for nitrogen credit generated from
the legume crop. For this term, the 50 lbs/acre is included in the total nitrogen recommendation
because the credit is accounted for in the term credits for plant available nitrogen in the field by year
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.1. Site-Specific Terms: Linear and Narrative Rate Approaches

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NPDES Permit Writers’ Manual for CAFOs

for the linear approach. See Section 6.6.2 below under, Credits for Plant Available Nitrogen and
step 6 of the Methodology in Section 6.6.3 for an example of how this credit was accounted for.
The phosphorus fertilizer recommendation for all crops is 0 lbs P2O5/acre. This is based on the
high phosphorus soil tests (Tables 6.3 of the sample NMP). Because the soil test recommendation
is zero and the appropriate nutrient rate basis, as defined by the outcome of the field specific risk
assessment, allows for phosphorus to be applied at a phosphorus removal rate, the term for the
total phosphorus recommendation is based on removal rate for each specific crop.

6.6.2. Additional Site-Specific Terms: Linear Approach
Credits for Plant Available Nitrogen
Data sources:
1. Sample NMP:
a. Table 6.8, Field Nutrient Balance
i. For legume and residual credits
b. Table 6.9, Field Nutrient Status Details
i. Also identifies residual manure Nitrogen credits
ii. Also can be used to identify adjustments to crop Nitrogen recommendations for
legume credits
2. Technical Standard:
a. Footnote “t” of the Iowa DNR Manure Management Plan Form
i. For legume credit values
b. Appendix B3 of the Iowa DNR, Manure Management Plan Form. Note Appendix B3
is the Iowa State University Extension publication PMR1033 (September 2008) Using Manure Nutrients for Crop Production.
i. For residual Nitrogen credit values
Example term:
Field ID
Bob’s Farm South

Subfield ID

Year

Crop

PAN credits(lbs/acre)

8S

2010

Soybean

0

2011

Corn

50†

2012

Soybean

0

2013

Corn

50† + 2*= 52

2014

Soybean

0

† - Legume credits
* - Residual manure Nitrogen credits

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

A note on using the sample NMP and technical standard to develop the permit term:
When the first year of an NMP contains 0 lbs of PAN/acre, it is assumed that the field has not
received manure or been planted in legumes in recent history. For most existing fields, the first
year of the plan will include a PAN credit. For permit renewals, permit writers should check the
first-year PAN credit to ensure that it is consistent with the known cropping and land application
history for the field as reflected under the previous permit.
MMP accounts for legume credits by adjusting the crop nitrogen recommendation. Here, the
legume nitrogen carryover from the prior legume crop is captured as part of the term, PAN credits.
The methodology describes in greater detail how the numeric values for both legume and
residual manure nitrogen credits were derived for each year. (See Step 6 of the methodology in
Section 6.6.3.)

Consideration of Multi-Year Phosphorus Application
Data sources:
1. Sample NMP: Table 6.7, Planned Nutrient Applications; Table 6.8, Field Nutrient Balance
2. Technical Standard Reference: Appendix A9 of the Iowa DNR, Manure Management Plan
Form, Chapter 567—65.17(19)
Example term:
Field ID

Year

Crop

Consideration of multi-year
phosphorus

Bob’s Farm South – 8S

2010

Soybean

No

2011

Corn

Yes

2012

Soybean

N/A

2013

Corn

N/A

2014

Soybean

No

A note on using the sample NMP and technical standard to develop the permit term:
Manure was applied in the fall of 2010. (See Table 6.7, Planned Nutrient Applications). The
application is shown here as occurring in 2011 because the fall application is nutrients for the
crop planted in the spring of 2011. Table 6.8 of the sample NMP, Field Nutrient Balance, does not
state that the manure application is considered a multi-year application with a yes or no as it is
shown in the table above. What Table 6.8 illustrates is that phosphorus balance remains after a
manure application had been made to meet the crop phosphorus removal rate. Therefore, more
phosphorus has been applied than was removed by the crop. What also should be noted in Table
6.8 is that additional manure is not applied until the balance returns to zero.
The methodology describes in greater detail how this manure application meets the state
requirements for applying a multi-year phosphorus application. (See Step 9 of the methodology in
Section 6.6.3.)
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

Accounting for All Other Additions of Plant Available Nitrogen and
Phosphorus to the Field
Data sources:
1. Sample NMP: Table 6.7, Planned Nutrient Applications
2. Technical Standard Reference: Not applicable
Example term:

Field ID

Available N
(Lbs/Acre)

Available
P202
(Lbs/Acre)

Subfield ID

Date

Other additions
of PAN

8S

2010

None

0

0

2011

Commercial fertilizer
(28-0-0)

128

0

2012

None

0

0

2013

Commercial fertilizer
(28-0-0)

158

0

2014

None

0

0

Bob’s Farm South

A note on using the sample NMP and technical standard to develop the permit term:
The only additional plant available nutrients that are applied to this field are nitrogen fertilizer.
The amount of available nitrogen from nitrogen fertilizer is shown in the table below, but the
value of available nitrogen is not part of the term and may fluctuate from year to year. The term
is the source of additional nutrients planned for each year and the fact that it is an additional
amount of nutrients necessary to ensure crop yield goals are met without exceeding maximum
limits, that is taken into consideration.

Form and Source of Manure that is Applied
Data source:
1. Sample NMP:
a. Table 6.7 Planned Nutrient Applications
i. Nutrient source
b. Table 2.3 Manure Storage
i. Type of storage
2. Technical Standard Reference: Not applicable

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

Example term:
Field ID

Subfield ID

Timing

Form

Source

8S

Fall 2010

Solid

E Lots Stack #1

Fall 2014

Solid

W Lots Stack #2

Bob’s Farm South

A note on using the sample NMP and technical standard to develop the permit term:
Timing is not a component of the term form and source of manure, litter, and process wastewater to
be land applied, but is included here to clarify the form and source to be applied at different times
during each crop year. For example, if the facility planned to apply liquid manure in the spring of
2011 and solid manure in the fall of 2011, the terms for timing and form would work in conjunction
to clarify the details for each manure application.
THe sample NMP does not specify the form of manure to be applied; however, according to the
information in Tables 2.3 (Manure Storage) and 6.7 (Planned Nutrient Applications), the permit
writer is able to determine the form of manure that is stored in each source.

Method and Timing of Land Application of Manure for Each Field
Data source:
1. Sample NMP: Table 6.7, Planned Nutrient Applications
2. Technical Standard Reference: Not applicable
Example term:
Field ID
Bob’s Farm South

Subfield ID

Timing
in NMP

Timing
term

Method

8S

Nov 2010

Fall 2010

Dry Box Spreader, Not incorporated

Sept 2014

Fall 2014

Dry Box Spreader, Not incorporated

A note on using the sample NMP and technical standard to develop the permit term:
MMP reports timing of applications on a monthly basis. Other tools might report an exact
date of application. That information can be captured more broadly as the permit term. Here,
it is captured on a seasonal basis. For this example, spring is defined as March, April, and
May. Summer is defined as June, July, and August. Fall is defined as September, October, and
November. Winter is defined as December, January, and February.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

Maximum Amount of Nitrogen and Phosphorus from Manure,
Litter, and Process Wastewater
Data source:
1. Sample NMP: Table 6.7, Planned Nutrient Applications
2. Technical Standard Reference: Not applicable
Example term:

Field ID

Max N from
manure applied

Max P202 from
manure applied

Subfield
ID

Crop
year

Crop

8S

2010

Soybean

0

0

2011

Corn

32

190

2012

Soybean

0

0

2013

Corn

0

0

2014

Soybean

0

0

Bob’s Farm South

(lbs/acre)

As indicated above, although the NMP shows the first manure application on this field in the fall
of 2010, that application is made for the corn crop to be planted in the spring of 2011, so the limits
are associated with the 2011 crop year. That is also true for the September 2014 manure applica­
tion. (Note that the Target Crop indicated in Table 6.7 for the November 2010 and September 2014
manure applications are corn, whereas the crops grown in 2010 and 2014 are soybeans.)
The permit term for the linear approach is the manure nutrients predicted by the NMP to be
applied expressed as pounds of nitrogen and phosphorus for each year of permit coverage. Note
that this value does not include residual nitrogen from previous application(s).
The operator has chosen not to meet crop needs solely with manure nutrients. Manure could
have been applied to the soybean crops, but the operator has chosen not to apply nutrients
in those three crop years (additionally, this plan has utilized the flexibility of a multi-year
phosphorus application which restricted any additional phosphorus from being applied until
the phosphorus from the multi-year application had been utilized by the crops). Also, the NMP
shows that commercial fertilizer will be applied to this field in addition to manure in 2011 and
2013. So, although the plan could have been written to allow more nutrients from manure to
be applied, the operator has chosen to limit manure application on this field. As described in
Section 6.5 under the linear approach, the NMP that is submitted with the NOI is the NMP that
is to be implemented over the 5 years of permit coverage. The permit terms are written to reflect
what is predicted by the submitted NMP. For the linear approach, the CAFO’s permit will limit
manure application on the basis of the amount of manure nutrients to be applied as predicted in
the submitted NMP, unless the operator follows the substantial change procedures to increase
this term.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

Methodology to Account for the Amount of Nitrogen and
Phosphorus in the Manure to be Applied
The term is the set of calculations used by the MMP software program to account for the amount
of nitrogen and phosphorus in the manure that is to be applied. That is the methodology used to
derive the amount of manure to be applied according to the term maximum pounds of nitrogen
and phosphorus from manure and the manure nutrient analysis. In this specific example, for the
2011 corn crop, 1,514 tons of dry box spreader manure from E Lots Stack #1 (that was not incorpo­
rated) was able to supply 32 pounds of nitrogen and 190 pounds of phosphorus. The permitting
authority has determined that this program accounts for the nitrogen and phosphorus in the tons
of manure to be applied. The term that is captured in the permit would be Use of Manure Management Planner, version 0.29. If the result of the annual manure nutrient analysis is different from
that used to develop the plan, the CAFO operator would use MMP to recalculate the amount of
manure to apply in 2010 and 2014 based on the term maximum amount of nitrogen and phosphorus from manure.
For this example field, the methodology for the linear rate approach is encompassed within the
methodology for the narrative rate approach. For a more detailed discussion on how the amount
of nitrogen and phosphorus in the manure applied is calculated, see steps 7.1 through 7.3.4 of the
methodology in Section 6.6.3.
Data source/Location in NMP:
1. Sample NMP: If MMP or other software is used, the methodology can be cited as use
of the program, if the permitting authority determines that the program adequately
accounts for the nitrogen and phosphorus in the manure to be applied.
Putting together all the terms that are applicable to the linear approach :
The methodology is expressed within MMP version 0.29. The permitting authority determined
that the methodology used by MMP was developed in accordance with the state’s technical
standard. Additional site-specific permit terms for expressing protocols for land application under
the linear approach are shown below. (Note that in this example, the permit term for the outcome
of the field risk assessment, was written so that a single risk was applied to the entire field.) For this
example, the terms are shown only for the field Bob’s Farm South, Subfield 8S, but a permit writer
for this facility would identify terms for all fields identified in the NMP.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

Fields
available
for land
application
SubField field

Outcome of the assessment
of the potential for nutrient
transport
Crop
year

Bob’s Farm South

Field slope 7%. Manure
Low
Manure shall not be Soybean
applied in excess of
may only be surface
applied to this field when
the nitrogen needs
the ground is frozen,
of the crop
snow covered or saturated
Medium Manure shall not be
Corn
if one of the following
applied in excess of
conditions exists:
two times the crop
Medium phosphorus removed Soybean
1. Where manure storage
with crop harvest
capacity is insufficient
over the period of
and failure to surface
Medium
Corn
the crop rotation
apply creates a risk of an
uncontrolled release of
manure
Medium
Soybean

61
bu/acre

P loss
risk

Timing limitations
for a land application

2011
8S

Realistic
annual
yield
goal

Total
acres

2010

2012

Planned
crops or
other
use

79.6

2013
2014

Allowable manure
application rate

2. On an emergency basis

Subfield

8S

Subfield

8S

195
bu/acre
61
bu/acre
195
bu/acre

Total nitrogen and
phosphorus
recommendations
for each crop on
each field

Soybean
recommendations
232 lbs N/acre
49 lbs P2O5/acre
Corn
recommendations
210 lbs N/acre
73 lbs P2O5/acre

61
bu/acre

Accounting for all other additions of plant
available nitrogen and phosphorus to the field

Crop
year

Credits for
PAN
lbs/acre

Consideration of multi-year
phosphorus application

PAN

P205

2010

0

No

None

None

2011

50

Yes; 3 years’ worth of manure phosphorus
is applied, and no additional phosphorus is
applied for the next two years.

Commercial fertilizer
(28-0-0)

None

2012

0

Continued

None

None

2013

52

Continued

Commercial fertilizer
(28-0-0)

None

2014

0

No

None

None

Crop
year

Form of
manure
applied

Source of
manure
applied

Timing
of land
application

2010

Solid

E Lots Stack #1

Fall

2011

No manure
applied

No manure
applied

2012

No manure
applied

2013
2014

Maximum amount of nitrogen
and phosphorus from manure
Method of land
application

N (lbs/acre)

P2O5 (lbs/acre)

Dry Box Spreader,
not incorporated

0

0

No manure
applied

No manure applied

32

190

No manure
applied

No manure
applied

No manure applied

0

0

No manure
applied

No manure
applied

No manure
applied

No manure applied

0

0

Solid

W Lots Stack #2

Fall

Dry Box Spreader,
not incorporated

0

0

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.2. Additional Site-Specific Terms: Linear Approach

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NPDES Permit Writers’ Manual for CAFOs

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach
As previously mentioned, six site-specific terms apply when using either the linear or narrative
rate approach for expressing land application rates in NMPs. Those six terms are (1) the fields
available for land application, (2) timing limitations for land application, (3) the outcome of the
nitrogen and phosphorus transport risk assessment, (4) planned crops or other use, (5) realistic
annual crop yield goal, and (6) total nitrogen and phosphorus recommendations for each crop.
Those permit terms for this sample NMP are identified in Section 6.6.1. The only exception is for
how the outcome of the nitrogen and phosphorus transport risk assessment would be reported.
Under the narrative rate approach, a single risk method would likely be utilized by the permit
writer. In addition to those six permit terms, the narrative rate approach has three additional sitespecific permit term requirements that are as follow:

Maximum Amount of Nitrogen and Phosphorus from All Sources
of Nutrients
Data Source:
1. Sample NMP: Table 6.7. Planned Nutrient Applications
Example term:

Field ID
Bob’s Farm South

Max N
Derived from all
sources

Subfield
ID

Year

Crop

8S

2010

Soybean

2011

Corn

2012

Soybean

2013

Corn

2014

Soybean

Max P205
Derived from all
sources

(lbs/acre)
Soybeans =
0 lbs N/acre

Soybeans =
0 lbs P205/acre

Corn =
210 lbs N/acre

Corn =
190 lbs P205/acre

The maximum amount of phosphorus from all sources in any single year is shown in Table 6.7 as
190 lbs/acre. (There is a 2014 fall application of manure that contains 200 lbs P2O5/acre but that is
targeted for crop in the next permit cycle.) The state’s P-Index interpretation of the medium risk
category is two times the crop phosphorus removed with crop harvest over the period of the crop
rotation. That would be 2 × (49 lbs P2O5/acre for soybeans plus 73 lbs P2O5/acre for corn) or 244 lbs
P2O5/acre (see step 4.4 of the methodology in Section 6.6.3 below). The NMP was not submitted
with any one crop receiving an application rate with 244 lbs P2O5/acre being applied. Therefore,
while a maximum amount of phosphorus from all sources could have been set at 244 lbs P2O5/
acre for any one crop, the plan was submitted with a maximum application rate of phosphorus
at 190 lbs P2O5/acre. Additionally, the state’s technical standards allow manure or other organic

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

6-76

NPDES Permit Writers’ Manual for CAFOs

by-products to be applied on legumes at rates equal to the estimated removal of nitrogen in the
harvested portion of the crop that is removed from the field in that growing season (Iowa NRCS
590). In this case, that would be 232 lbs nitrogen/acre for the soybean crop. Therefore, a maximum
amount of nitrogen could have been set at 232 lbs nitrogen/acre for soybeans. The NMP was not
submitted with any soybean crop receiving an application rate with 232 lbs nitrogen/acre being
applied. Therefore, while a maximum amount of nitrogen from all sources could have been set at
232 lbs nitrogen/acre for soybeans, the plan was submitted with a maximum application rate of
nitrogen at 0 lbs nitrogen/acre.
As noted in Section 6.5.3, the maximum rates of nitrogen and phosphorus are not associated with
a particular year. They are associated only with a particular crop. The rates could be applied in
any one year as long as no other permit terms or conditions are violated.

Alternative Crops
The term is the alternative crops (in addition to the planned crops) listed in the NMP. In this plan,
there are no alternative crops being grown.
Data source: N/A – The example plan does not include any alternative crops. However, if it were to
include crops, the term could be reported as follows:
Example term:

Field

N rec.

P2O5 rec.

Subfield

Potential alternative
crop(s)

Yield goal
(unit/acre)

8S

Wheat

78 bu/acre

88

41

Alfalfa

4.1 ton/acre

205

51

Bob’s Farm
South

(lbs/acre)

Methodology
Data source: In the sample NMP, the methodology is expressed within MMP version 0.29. The
permitting authority determined that the methodology used by MMP encompasses all the
factors of the methodology, and the plan was developed in accordance with the state’s technical
standard.
The steps described below review development of the application rates for the entire permit cycle
for the field Bob’s Farm South, Subfield 8S from the sample NMP. The steps review the entire
process of calculating land application rates to show how the methodology should account for the
required narrative rate factors; therefore, the steps repeat some of the information on narrative
rate approach terms described above. In addition, the methodology presented here is useful to
illustrate the general process for calculating land application rates, regardless of whether the
linear or narrative rate approach is used.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Several of the narrative rate factors are addressed in multiple steps in the process below, as
follows:
Factor

Step(s)

Soil test results

3.1

Credits for PAN in the field

6

Total amount of nitrogen and phosphorus in the manure to be applied

7

Consideration of multi-year phosphorus application

9

Accounting for all other additions of plant available nitrogen and phosphorus
to the field

5

Form and source of manure

7.1

Timing and method of land application

7.3.2

Volatilization of nitrogen and mineralization of organic nitrogen

7.3.2 and 6.2

These steps should serve as guidance for permitting authorities as to what EPA expects of various
nutrient management planning programs to ensure that they encompass all the required factors
of the methodology. The methodology can be rather complicated, and a step by step approach
does not necessarily always need to be written out in its entirety as a permit term. As stated
earlier, it is common for much of the methodology to be embedded within many state software
programs. However, the process below and the type of information that it captures should be
contained within all methodologies. In addition, software documentation that clearly describes
the methodology should be made publicly available.
The steps below outline the process to account for the required factors of the narrative rate
methodology; therefore, the term outcome of the nitrogen and phosphorus transport risk
assessment is expressed as a single risk rating for a field according to the highest crop year’s risk.

Step 1: Identify the Technical Standards Applicable to the Plan for
Developing Rates of Application
The sample plan is for a facility in Sioux, Iowa. The sample technical standard that applies to this
location is in Appendix O, Sample Site-Specific NPDES General Permit.

Step 2: Identify the Fields where Manure Nutrients Will be Applied
Manure is planned to be land applied in crop years 2011 and 2015, with actual application in the
fall of 2010 and 2014, or permit years 1 and 5 (2010–2014) to Bob’s Farm South Subfield 8S (field 8S
from here onward).

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Field
Bob’s Farm South

Subfield

Crop year

Application rate

Units

8S

2010

0

N/A

2011

1,514

Tons

2012

0

N/A

2013

0

N/A

2014

0

N/A

2015

1,500

Tons

These values are found in Table 6.7, Planned Nutrient Application of the sample NMP. In Table 6.7,
two applications are shown to occur in November of 2010 and November of 2014. Those are
considered nutrient applications for the following calendar year; spring crop 2011 and spring
crop 2015. While 2015 is not part of this permit cycle and would not be captured as part of this
permit’s permit terms, it is shown here as it would be necessary to account for that information
during the next permit cycle. The nutrient applications are not themselves a term; however, the
methodology for calculating them is. The tons or gallons of manure applied should follow the
basic methodology:
Manure nutrients applied ≤ Max nitrogen or phosphorus from all sources – other additions of
plant available nutrients – available in field nutrients
The required factors of the narrative rate methodology can be found within those four variables.
Calculating the value of each variable above takes into consideration the other required factors of
the narrative rate approach. The process below illustrates how all the factors of the methodology
are included in the NMP and used in calculating the tons and gallons of manure to be applied.

Step 3: Identify the Allowable Basis for Calculating an Application Rate
Because manure, litter and process wastewater contain both nitrogen and phosphorus, the
application of manure to each field will be made so that the appropriate amount of nutrients
are supplied to meet either the nitrogen or phosphorus requirement of the crop being grown
on that field. This is determined by the outcome of field specific assessment for the potential
of phosphorus transport from each field. The specific risk assessment used is provided in the
sample state technical standard for nutrient management. Because the sample NMP is based on
an operation that is in Iowa, the sample technical standard used for Iowa requires that the Iowa
P-Index (as specified by the USDA NRCS Iowa Technical Note no. 25) be used to determine the
nutrient basis for all manure applications. The Iowa P-Index calculations result in a numerical
value that corresponds to one five risk assessments:

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

6-79

NPDES Permit Writers’ Manual for CAFOs

Total points
from index

Interpretation
of points

0–1

Very Low

Manure shall not be applied in excess of an nitrogen-based
rate in accordance with 65.17(18)

> 1–2

Low

Manure shall not be applied in excess of an nitrogen-based
rate in accordance with 65.17(18)

> 2–5

Medium

Manure shall not be applied in excess of two times the
phosphorus removed with crop harvest over the period of
the crop rotation.*

> 5–15

High

> 15

Very High

Basis for application rate

Manure shall not be applied until practices are adopted
which reduce the P-Index to at least the medium risk
category.
Manure shall not be applied.

* Regulations 65.17(17) describe the manure application rate requirements for fields that are assigned the
P-Index site vulnerability ratings described by the Iowa P-Index. The sample technical standard does not
always restrict applications on a field with a medium risk rating to 2 times the crop phosphorus removal
rate. However, for this example, 2 times the phosphorus removed with crop harvest over the period of the
crop rotation is set as the upper limit for all medium risk ratings.

The Iowa P-Index uses source and transport factors to approximate phosphorus loads to surface
waters. The source factors are arranged in a multiplicative manner within three components that
represent the main transport mechanisms: (1) Erosion Component (sediment loss), (2) Runoff
Component (water loss), and (3) Subsurface Drainage Component (water movement through tile
or coarse subsoil/substrata). The Iowa P-Index is calculated as follows:
Erosion component + Runoff component + Subsurface drainage component = P-Index
The three components are composed of the following variables:
1. Erosion =
Gross erosion × (sediment trap factor or delivery ratio) × buffer factor × enrichment factor
× Soil Test Phosphorus (STP) erosion factor
2. Runoff =
Runoff factor × precipitation × (STP runoff factor + phosphorus application factor)
3. Subsurface drainage =
Precipitation × flow factor × STP drainage factor

Step 3.1: Use the Soil Test Results to Calculate the Outcome of the Risk
Assessment
STP, a required factor of the methodology, is considered in all three transport components of the
Iowa P-Index.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

The soil test results are shown in Table 6.3, Soil Test Data, of the sample NMP. The results are as
follows:
Field
Bob’s Farm South

Subfield

Test year

P concentration

Units

Test analysis

8S

2009

32

ppm

Bray P1

The outcome of the assessment is provided Table 5.3, Nitrogen and Phosphorus Risk Analysis,
of the sample NMP. In this example, the P-Index is run each year for each crop on the field. The
permit term is based on the highest risk for each crop over the course of the 5 years of permit
coverage. In this case, the highest risk is a medium risk (for both corn and soybeans), which limits
application rates to two times the phosphorus removed with crop harvest over the period of the
crop rotation.

Field ID
Bob’s Farm South

Subfield
ID

Year

Risk

Basis for
application rate*

8S

2010

Low

Nitrogen-based

2011

Medium

2 times the phosphorus removed with
crop harvest over the period of the
crop rotation.

2012

Medium

2 times the phosphorus removed with
crop harvest over the period of the
crop rotation.

2013

Medium

2 times the phosphorus removed with
crop harvest over the period of the
crop rotation.

2014

Medium

2 times the phosphorus removed with
crop harvest over the period of the
crop rotation.

* The basis for the allowable application rate is not provided in Table 5.3 of the sample NMP. The appropriate
rate basis was identified from the technical standard and applied to the appropriate risk category.

Step 4: Derive the Crop Nutrient Requirements
Crop nutrient requirements are derived from the planned crops, their realistic yield goals, and
the total nitrogen and phosphorus recommendation for each crop identified in the planned
crop sequence. The permit terms for field 8S, for planned crops, yield goals, and total nitrogen
and phosphorus recommendations are shown below. Table 6.5 in the sample NMP identifies
the Planned Crops and Fertilizer Recommendations as well as the crop removal rates. Steps 4.1
through 4.3 illustrate how the values in total nitrogen and phosphorus recommendations were
determined.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Year

Field crop

Yield goal
(bushels/
acre)

Total recommended
nitrogen (lbs/acre)

Total recommended
phosphorus
(lbs per/acre)

2010

Soybean

61

232

N/A

2011

Corn

195

210

73

2012

Soybean

61

232

49

2013

Corn

195

210

73

2014

Soybean

61

232

49

Step 4.1: Derive the Realistic Annual Yield Goals
All crop recommendations are based on a realistic yield goal for the crop. The yield goal typically
represents the expected optimum yield for that crop. The example plan, as written, does not
provide a specific reference for how the yield goal was determined. The regulations do not require
that an NMP provide the basis for the yield goal; however, the permit writer has the authority
to request the source of that information, which might be necessary if the values appear to be
unrealistic. The sample technical standard provides multiple options for calculating an optimum
yield goal. Those include the following:
▶ Soil survey interpretation record.
▶ USDA county crop yields.
▶ Proven yield methods. Proven yield methods may be used only if a minimum of the
most recent three years of yield data for the crop is used. Those yields can be proven
on a field-by-field or farm-by-farm basis. Crop disaster years may be excluded when
there is a 30 percent or more reduction in yield for a field or farm from the average
yield over the most recent five years. Excluded years shall be replaced by the most
recent non-disaster years. Proven yield data used to determine application rates
shall be maintained with the current manure management plan.
A review of the yield goals provided in the sample NMP shows that USDA county crop yields were
used. The sample technical standard contains Iowa Ag Statistics for County Corn and Soybean
Yields. The 5-year average yield, the 5-year average yield +10 percent and the average yield of the
four highest years are provided. For Sioux County, the location of the facility for which the sample
plan was developed, the 5-year average yield +10 percent is 195.3 bu/acre for corn and 60.7 bu/
acre for soybeans, which matches the reported sample NMP yield goals for corn and soybeans.

Step 4.2: Derive the Crop Nitrogen Recommendations
The sample technical standard provides Crop Nitrogen Usage Rate Factors for Various Crops. For
corn, those nitrogen usage rate factors are based on the expected yield goal and the appropriate
geographic zone where corn is being grown. The standard outlines three geographic zones for

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

6-82

NPDES Permit Writers’ Manual for CAFOs

different soil associations. The sample NMP is written for an operation in Sioux County, which is
in both zones 1 and 2. The nitrogen usage rate factor for zone 1 is 0.9 lbs N/bu, and the nitrogen
usage rate factor for zone 2 is 1.1 lbs N/bu. The estimated yield goal for corn is 195 bu/acre.
Zone 1 Nitrogen Usage Rate = 195 bu/acre × 0.9 lbs N/bu = 176 lbs N
Zone 2 Nitrogen Usage Rate = 195 bu/acre × 1.1 lbs N/bu = 215 lbs N
The NMP includes an nitrogen recommendation of 210 lbs nitrogen/acre. Because Sioux
county contains both zone 1 and zone 2 nitrogen usage factors, a nitrogen recommendation
of 210 appears to be appropriate. If the permit writer believes that the nitrogen or phosphorus
recommendation in the NMP is significantly different than that which can be derived from the
technical standard, it is a good idea to ask the operator or planner to explain the basis for the rate.
Note that Table 6.5 of the sample NMP does not show a corn nitrogen recommendation of 210 lbs
nitrogen/acre. When corn follows a legume, the crop need is shown as 50 lbs less than the total
nitrogen recommendation. That is because the nitrogen credits from the legume crop are directly
factored into the recommendation in Table 6.5. For purposes of identifying permit terms, the total
nitrogen recommendation will still be identified as 210 lbs nitrogen/acre. The 50 lbs of nitrogen
credit from the legumes will be accounted for under the factor all other plant available credits in
the field, shown in step 6 below.

Step 4.2.1: Derive the Crop Nitrogen Removal Rates
The sample technical standard allows for manure or other organic by-products to be applied
on legumes at a rate equal to the estimated amount of nitrogen in the harvested portion of the
crop that is removed from the field in that growing season (i.e., crop nitrogen removal). The
nitrogen removal for soybeans is 3.8 lbs nitrogen/bushel (found in sample technical standard,
Appendix A6 of the Manure Management Plan Form). MMP’s Initialization File Summary Report
also includes that information and could be provided with the CAFO’s NMP (see Section 8.3 of the
sample NMP). Given the expected yield goal of 61 bushels/acre, the allowable nitrogen application
is 232 lbs/acre.
3.8 lbs N/bushel × 61 bushels/acre = 232 lbs N/acre
Table 6.5 in the sample NMP also provides that removal rate for soybeans. Although the fertilizer
nitrogen recommendation for soybeans is 0 lbs of nitrogen, the permit term Total nitrogen
recommendation is 232 lbs nitrogen/acre based on the technical standard allowance for nitrogen
application on legume crops.

Step 4.3: Derive the Crop Phosphorus Recommendations
The term total phosphorus recommendation is based on the removal rate of each crop. Removal
rates are found in the sample technical standard, Appendix A6 of the Manure Management Plan
Form and in MMP’s Initialization File Summary Report (see Section 8.3 of the sample NMP). For
corn, the removal rate is 0.375 lbs P/yield unit, and for soybeans it is 0.8 lbs P/yield unit.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Corn
0.375 lbs P2O5/bushel × 195 bushels = 73 lbs P2O5
Soybean
0.8 lbs P2O5/bushel × 61 bushels = 49 lbs P2O5/acre
Table 6.5 of the sample NMP also provides those removal rates for corn and soybeans.

Step 4.4: Determine the Maximum Amount of Crop Nutrient from All Sources
The methodology relies on the maximum amount of crop nutrients that could be applied from all
sources for illustrating the basic methodology:
Manure nutrients applied ≤ Max nitrogen or phosphorus from all sources—other additions of
plant available nutrients—available in field nutrients
The permit term is based on what is shown in the NMP as submitted with for permit coverage. As
discussed in Section 6.6.3, it was identified that for this field, nutrient application rates were not
set as the maximum possible rate as allowed under the state’s technical standard. The maximum
amount of nutrients that could have been applied is used to illustrate that permit terms are in
compliance with the state’s technical standards for nutrient management.
The maximum amount of nitrogen that can be applied from all sources is equal to the amount of
nitrogen identified for the permit term, total nitrogen recommendation.
The maximum amount of phosphorus from all sources that can be applied is based on the term,
outcome of the field-specific risk assessment. For field 8S, the Iowa P-Index results in a medium
risk. The state standards define the phosphorus limit for medium-risk fields as two times the crop
phosphorus removed over the crop rotation. Field 8S shows a corn, soybean rotation.
Corn:
73 lbs P2O5 removed/acre
Soybean:
49 lbs P2O5 removed/acre
2 × (49+73 lbs P2O5/acre) = 244 lbs P2O5/acre
Applying those values to the basic methodology is described as
Manure nutrients applied ≤ Max nitrogen or phosphorus from all sources - other additions of
plant available nutrients—available in field nutrients

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

6-84

NPDES Permit Writers’ Manual for CAFOs

Crop Year 2010, 2012, and 2014: Soybeans
X lbs N/acre from manure ≤ 232 lbs N/acre - commercial fertilizer applied lbs N/acre - N available
in field lbs/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - commercial fertilizer applied lbs P2O5/acre - P2O5
available in field lbs/acre
Crop Year 2011 and 2013: Corn
X lbs N/acre from manure ≤ 210 lbs N/acre - commercial fertilizer applied lbs N/acre - N available
in field lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - commercial fertilizer applied lbs P2O5/acre - P2O5
available in field lbs/acre

Step 5: Determine Other Sources of Nutrients Applied
The term accounting for all other additions of plant available nitrogen and phosphorus to the field
captures the amount of nutrients from sources other than manure. Those nutrients are applied
to the total amount required to meet the crop’s need. That includes nutrient sources such as
commercial fertilizers, biosolids, or irrigation water. According to the sample NMP, commercial
fertilizer is the only source of nutrients added besides manure. That can be found in Table 6.7 of
the sample NMP. Commercial fertilizer is added to subfield 8S in years 2011 and 2013. Adding
that to the basic methodology is as follows (with the amount of nutrients from sources other than
manure shown as the second element of the expression):
Crop Years 2010, 2012, and 2014: Soybeans
X lbs N/acre from manure ≤ 232 lbs N/acre - 0 lbs N/acre - N available in field lbs/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - 0 lbs P2O5/acre - P2O5 available in field lbs/acre
Crop Year 2011: Corn
X lbs N/acre from manure ≤ 210 lbs N/acre - 128 lbs N/acre - N available in field lbs/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - 0 lbs P2O5/acre - P2O5 available in field lbs/acre
Crop Year 2013: Corn
X lbs N/acre from manure ≤ 210 lbs N/acre - 158 lbs N/acre - N available in field lbs/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - 0 lbs P2O5/acre - P2O5 available in field lbs/acre

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

6-85

NPDES Permit Writers’ Manual for CAFOs

Step 6: Determine the Available in Nutrients in the Field
This step accounts for the PAN that is already in the soil from prior legume crops, previous
manure applications, and other sources. Credits for PAN in the sample NMP come from legumes,
which contribute nitrogen to the soil, and from the mineralization of organic nitrogen from
previous years’ manure applications.

Step 6.1: Accounting for Legume Credits
Soybeans are the only legume planted in field 8S. As mentioned in step 4, MMP accounted for
nitrogen credits from legumes by adjusting the recommendation for corn in years following a soy­
bean crop. Footnote ‘t’ of the Manure Management Plan Form in the sample technical standard
contains the appropriate credits for legume crops. Credits for nitrogen carryover from prior year
legume crops are calculated as follows:
▶ Credit 1 lb nitrogen per bushel of yield for the previous year’s soybean crop.
▶ A maximum credit of 50 lb nitrogen per acre is allowed.
Yield goal
(bushels/acre)

Total nitrogen legume
credit (lbs/acre)

Year

Field crop

2010

Soybean

61

0

2011

Corn

195

50

2012

Soybean

61

0

2013

Corn

195

50

2014

Soybean

61

0

Step 6.2: Accounting for Manure Mineralization Credits
Residual manure nitrogen credits are identified in the Field Nutrient Status Detail Custom Report,
provided in Section 6.9 of the sample NMP. Mineralization rates for organic nitrogen are defined
in the sample technical standard under Iowa State University Extension publication PMR1033 Using Manure Nutrients for Crop Production (September 2008). The technical standard provides
mineralization rates for the year of application and two years following manure application.

Animal type

1st year nitrogen
availability

2nd year nitrogen
availability

3rd year nitrogen
availability

Beef cattle (solid)

35%

10%

5%

The fraction of nitrogen from manure that will be available in year 1, when the manure is applied,
is not captured as a part of this credit. Credits are derived from only what is carried over from
a previous year’s application. Mineralized nitrogen available during the year of application is
accounted for in step 7 below.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

6-86

NPDES Permit Writers’ Manual for CAFOs

On subfield 8S, manure is first applied in 2011, which provides residual manure credits for years
2012 and 2013. Manure is also applied in year 2014, which creates credits for year 2015 and 2016.
Credits for year 2015 and 2016 fall under a new permit cycle and will be accounted for then.
Application

Nitrogen availability
1 year
availability
(35%)

2nd year
availability†
(10%)

3rd year
availability†
(5%)

2010

2011

2012

st

Application
year

Total manure
N* (tons/acre)

2010

0

2011

133

2012

0

2014

0

2015

140

0

0

2011

2012

32

10

2012

2013

0

0
2013
4
2014

0

2013

0

2014

0

2015

0

2014

2015

34

10

0
2016
5

* To calculate the total manure nitrogen applied, which is needed to determine residual manure credits, the manure analysis is
used. Derivation of this value is described in step 7.3.2.
† The second and third year availability estimates of 10 and 5 percent cannot be applied directly to the total manure nitrogen
applied to the field to determine nitrogen availability for the second and third years after land application. Volatilization losses
associated with manure application in year 1 must be accounted for first. Step 7.3.2 calculates the manure nitrogen available
after application, which accounts for volatilization losses and the first year manure nitrogen availability. The second and third
year availability estimates of 10 and 5 percent are applied to this nitrogen value after volatilization.

Combining the total PAN credits from step 6.1 and 6.2 (legumes and 2nd and 3rd year mineraliza­
tion credits) for each year as follows:
Permit year

Field crop

Total N credit
(as calculated) (lbs/acre)

Total N credit
(available) (lbs/acre)

2010

Soybean

0

0

2011

Corn

50

50

2012

Soybean

10*

0

2013

Corn

54*

52

2014

Soybean

0

0

2015

Unknown

0

0

2016

Unknown

10

10

2017

Unknown

5

5

* Residual credits are calculated as available in years 2012 and 2013 from the fall 2010 manure application. However, MMP
assumes that if the crop does not utilize the available nitrogen in the year that it is made available, it is lost. Table 6.8, Field
Nutrient Balance of the sample NMP shows a positive nitrogen balance of 2 extra lbs of nitrogen/acre in year 2013. Those two
excess nitrogen credits are assumed lost because they are not necessary to meet the corn crop needs. Therefore, only the 52
lbs of nitrogen credit/acre are utilized and reported.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

6-87

NPDES Permit Writers’ Manual for CAFOs

Years 2015–2017 are shown in the table above to capture residual manure nitrogen credits that
will be available from the 2014 fall application. These values are not included as part of this permit
cycle but will be important to know if this facility reapplies for a second permit cycle. Credits for
PAN available in the field are shown as the third element in the expressions below.
Crop Year 2010 and 2014: Soybean
X lbs N/acre from manure ≤ 232 lbs N/acre - 0 lbs N/acre - 0 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - 0 lbs P2O5/acre - 0 lbs P2O5/acre
Crop Year 2011: Corn
X lbs N/acre from manure ≤ 210 lbs N/acre - 128 lbs N/acre - 50 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - 0 lbs P2O5/acre - 0 lbs P2O5/acre
Crop Year 2012: Soybean
X lbs N/acre from manure ≤ 232 lbs N/acre - 0 lbs N/acre - 0 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - 0 lbs P2O5/acre - 0 lbs P2O5/acre
Crop Year 2013: Corn
X lbs N/acre from manure ≤ 210 lbs N/acre - 158 lbs N/acre - 52 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre - 0 lbs P2O5/acre - 0 lbs P2O5/acre

Step 7: Meeting the Remaining Nutrient Need with Manure
The preceding steps have illustrated how to calculate the amount of nutrients to be applied from
manure. The equations can now be simplified to
Crop Year 2010: Soybean
X lbs N/acre from manure ≤ 232 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre
Crop Year 2011: Corn
X lbs N/acre from manure ≤ 32 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre
Crop Year 2012: Soybean
X lbs N/acre from manure ≤ 232 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

6-88

NPDES Permit Writers’ Manual for CAFOs

Crop Year 2013: Corn
X lbs N/acre from manure ≤ 0 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre
Crop Year 2014: Soybean
X lbs N/acre from manure ≤ 232 lbs N/acre
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre
Steps 7.1 through 7.4 use the remaining factors of the methodology to illustrate how the remaining
nutrient needs can be satisfied with the nutrients from manure applications. The remaining
factors include the form and source of the manure that is applied, the timing and method of
manure application, the amount of nitrogen that volatilizes, and the nitrogen and phosphorus in
the manure analysis.

Step 7.1: Identify the Form and Source of the Manure that is Applied
The form and source of manure to be applied to must be identified in the NMP. One reason is
to ensure that the appropriate manure analysis is used. The form and source of manure is in
Table 2.3, Manure Storage of the sample NMP. The results are as follows:
Source

Form

E Lots Stack #1

Solid

E SetldSolidBasin #3

Solid

E Storage Pond #1

Liquid

W Lots Stack #2

Solid

W SetdSolidBasin #4

Solid

W Storage Pond #2

Liquid

The form can be identified as a liquid or a solid depending on the rate at which it is applied, pounds
or tons for solid and gallons for liquids as is indicated in the planned nutrient application table.
Field 8S has two applications, one in the fall of 2010 and one in the fall of 2014. As mentioned, both
of those applications are credited toward the next year’s spring crop and are therefore considered
applications for the permit year 2011 and 2015. The fall 2010 application comes from the solid
manure held in the E Lots Stack #1, and the fall 2014 application comes from the solid manure
held in the W Lots Stack #2.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Step 7.2: Reading the Manure Analysis
The amount of nitrogen and phosphorus contained in the manure is determined by the manure
analysis. The manure analysis is in Table 6.4 of the sample NMP. A manure analysis is provided
for each manure source. In this sample NMP, for field 8S, manure is used from E Lots Stack #1
and W Lots Stack #2. These two manure storage structures have the same manure analysis. The
manure analyses for all manure sources are as follows:
Measured
total
nitrogen

Measured
NH4 -N

Measured
Total P2O5

E Lots Stack #1

7.0

2.6

10.0

lbs/ton

W Lots Stack #2

7.0

2.6

10.0

lbs/ton

Source

Units

Step 7.3: Calculate the First Year Nitrogen Availability
The nitrogen content that is measured by the manure analysis is not what is available to the crops
when applied to the field. Only a portion of the nitrogen will mineralize and become available
in year 1 (as discussed in step 6.2). Additionally, the amount of nitrogen that is applied is subject
to volatilization losses. The following steps go through each of those processes to determine the
amount of nitrogen that is applied and available to the crops for uptake.

Step 7.3.1: Accounting for the Storage and Handling of Manure
Volatilization of nitrogen will occur during the handling and storage and the manure. Those
losses are already accounted for in the measured manure analysis shown above. As discussed in
Chapter 5, the manure analysis should be taken as close to the time of application as possible to
accurately assess the nutrient content just before field application to reflect these types of losses.

Step 7.3.2: Accounting for the Timing and Method of Land Application
Different methods of land application affect the amount of nitrogen that will volatilize. This must
be taken into consideration so the concentration of available nitrogen in the manure that is being
land applied can be estimated accurately. It is important to remember that only the ammonium
fraction of the total nitrogen value volatilizes. However, the applicable technical standard for the
sample NMP applies the volatilization factor to the total nitrogen value from the manure analysis.
This is not necessarily how all technical standards calculate nitrogen availability.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Year

Manure
applied
(tons)

Total
manure
nitrogen*
(lbs/acre)

Method of
application

Timing of
application

Volatilization
correction
factor†

Manure
nitrogen
after
application
(lbs/acre)‡

N/A

N/A

N/A

0

Dry Box
Spreader

Not
incorporated

0.7

93

2010

0

0

2011

1,514

133

2012

0

0

N/A

N/A

N/A

0

2013

0

0

N/A

N/A

N/A

0

2014

0

0

N/A

N/A

N/A

0

2015

1,500

140

Dry Box
Spreader

Not
incorporated

0.7

98

* Total Manure Nitrogen is calculated as follows:
(Tons applied × Total Manure Nitrogen analysis)/acres manure spread
Example: Year 2011 total manure nitrogen = (1,514 tons × 7.0 lbs N/ton) / 79.7 acres = 133 lbs N/acre
† From the sample technical standard, Iowa State Extension PMR 1003 – Using Manure Nutrients for Crop Production provides
volatilization rates for manure application. PMR 1003 specifies that when solid manure is broadcast and not incorporated the
manure total nitrogen rate applied should be multiplied by the volatilization correction factor of 0.70 to 0.85 to determine
the portion of total manure nitrogen remaining. Because manure applied in year 2011 was not incorporated, MMP applied a
0.70 volatilization correction factor.
‡ Step 7.3.2 accounts for the ammonium nitrogen that volatilizes from the total manure nitrogen because of the method of
application. Step 7.3.3 shows how to calculate the portion of organic nitrogen that mineralizes in year 1 and is available for
plant uptake.

Step 7.3.3: Calculating the Mineralization of Nitrogen
The nitrogen in manure is available over multiple years. The sample technical standard uses Iowa
State University Extension publication PMR1033 (September 2008), Using Manure Nutrients for
Crop Production, to estimate the amount of manure nitrogen, by animal source, that is available
over the course of three years. This nitrogen availability must be taken into consideration when
determining the tons of manure to apply to meet the crop needs.
The technical standard includes a mineralization factor of 35 percent for the first year of
application. The first year mineralization estimate of 35 percent was applied the total manure
nitrogen after application as derived in step 7.3.2. The year 1, total available manure nitrogen
values are directly provided in the sample NMP, in Table 6.7 Planned Nutrient Applications
(Manure-Spreadable Area). It is important to remember that only the organic fraction of the total
nitrogen value mineralizes. (The organic nitrogen fraction can be calculated by subtracting the
ammonium nitrogen value from the total nitrogen value.) However, the applicable technical
standard for the sample NMP applies the mineralization rate to the total nitrogen remaining
after volatilization. This is not necessarily how all technical standards calculate manure nitrogen
availability.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Year

Manure nitrogen
after application
(lbs/acre)*

First year nitrogen
availability for beef
cattle manure

Year 1 plant
available manure
nitrogen
(lbs N/acre)

2010

0

N/A

0

2011

93

35%

32

2012

0

N/A

0

2013

0

N/A

0

2014

0

N/A

0

2015

98

35%

34

* Values calculated in step 7.3.2.

Step 7.3.4: Determining the Availability of Manure Phosphorus
The sample technical standard, Iowa State University Extension publication PMR1033 (September
2008), Using Manure Nutrients for Crop Production, indicates that phosphorus from beef cattle
manure is 60 to 100 percent available in the first year of application. For this example, based on
the methodology used in MMP, 100 percent of the total phosphorus from the manure nutrient
analysis is assumed to be plant available.

Year

Manure
applied
(tons)

Total manure
P2O5 after
application
(lbs/acre)*

First year N
availability
for beef cattle
manure

0

N/A

190

100%

Year 1 plant
available manure
P2O5 (lbs/acre)

2010

0

0

2011

1,514

2012

0

0

N/A

0

2013

0

0

N/A

0

2014

0

0

N/A

0

2015

1,500

200

100%

190

200

* Total Manure P2O5 after application is calculated as follows:
(Tons applied × Total Manure Phosphorus analysis)/acres manure spread
Example: Year 2011 total manure phosphorus = (1,514 tons ×10.0 lbs P2O5/ton)/79.7 acres = 190 lbs P2O5/acre

Step 8: Meeting the Remaining Crop Needs for Crop Years 2010 and 2011
Step 7 illustrated how to determine the actual amount of nutrients from the manure applied that
would be available after land application to meet the crop nutrient needs along with nutrients
available from other sources. Step 8 illustrates how the pounds of nutrients are converted to tons
of manure and how the manure that is planned to be applied is in compliance with the maximum
permit limits.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Step 8.1: Calculate Manure Application Rate for Crop Year 2010
As shown in Step 2, the NMP indicates that no manure will be applied in year 2010. Therefore,
0 Tons of manure = 0 lbs N/acre
and
0 Tons of manure = 0 lbs P2O5/acre
The NMP demonstrates compliance with the permit terms with respect to manure application
because:
0 lbs N/acre < 232 lbs N/acre
0 lbs P2O5/acre < 244 lbs P2O5/acre

Step 8.2: Calculate Manure Application Rate for Crop Year 2011
As shown in Step 5, commercial fertilizer application is planned for the 2011 corn crop. At the
beginning of Step 7, the equations demonstrate that manure nutrients could be used to supply up
to 32 lbs8 of nitrogen needed by the corn crop as long as the manure application is in compliance
with the medium field risk assessment and does not contain more than 244 lbs of P2O5.
X lbs of N/acre from manure ≤ 32 lbs N/acre
and
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre
As shown step 7, the NMP indicates that the CAFO plans to apply 1,514 tons of manure which will
supply 32 pounds of nitrogen per acre.
1,514 Tons of manure = 32 lbs manure N/acre
32 lbs manure N/acre = 32 lbs N/acre
Step 7 also shows that 1,514 tons of manure supplies 190 lbs of phosphorus therefore:
1,514 tons manure = 190 lbs P2O5/acre
190 lbs P2O5/acre < 244 lbs P2O5/acre
On the basis of that check, the 1,514 tons of manure planned for application is in compliance with
the permit limits. However, the permit writer should be aware that, although the crop phosphorus
removal rate for corn is 73 lbs of phosphorus, 190 lbs of phosphorus are being applied. Before
moving on to the remaining years, it will be imperative to determine that this application rate is
in compliance with the state’s technical standards for multi-year phosphorus application.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Step 9: Accounting for Multi-Year Phosphorus Application in Crop
Year 2011
The technical standards allow multi-year phosphorus application on fields that are limited to
a phosphorus-based application rate. The sample technical standard establishes the following
requirements for multi-year phosphorus application.
1. No single manure application shall exceed the nitrogen-based rate of the planned crop
receiving the manure application.
2. No single manure application shall exceed the rate that applies to the expected amount
of phosphorus removed with harvest by the next four anticipated crops in the crop
schedule.
3. If the actual crop schedule differs from the planned crop schedule, any surplus or deficit
of phosphorus shall be accounted for in the subsequent manure applications.
In 2011 on Subfield 8S, 1,514 tons of manure is planned to be applied to a corn crop; the manure
supplies 190 lbs/acre of P2O5. A single year of phosphorus removal for growing 195 bushels of corn
is 73 lbs/acre of P2O5. EPA defines multi-year phosphorus application as phosphorus applied to
a field in excess of the crop needs for that year. 190 lbs/P2O5 is more phosphorus than the crop
needs for 2011. However, this application appears to meet the state’s requirements for a multi-year
application based on the following:
1. The 1,514 tons of manure that is applied in November 2010 for the 2011 crop year supplies
32 lbs/acre of nitrogen which, in conjunction with other sources of PAN, does not exceed
the 210 lbs/acre of nitrogen recommended for this corn crop.
2. Assuming the crop rotation of soybean–corn continues with soybeans in year 2015, the
total amount of phosphorus removed by the crops for the next 4 years would total
Years 2012 soybeans = 0.8 lbs P2O5/bu × 61 bu/acre = 49 lbs/acre P2O5
Year 2013 corn = 0.375 lbs P2O5/bu × 195 bu/acre = 73 lbs/acre P2O5
Years 2014 soybeans = 0.8 lbs P2O5/bu × 61 bu/acre = 49 lbs/acre P2O5
Year 2015 corn = 0.375 lbs P2O5/bu × 195 bu/acre = 73 lbs/acre P2O5
TOTAL = 244 lbs/acre P2O5 allowed
The applied 190 lbs/acre P2O5 does not exceed this limit.
3. 190 lbs/acre P2O5 contains approximately the next 3 years’ worth of phosphorus that is
expected to be removed and from this NMP, it is shown that no additional phosphorus
will be applied for the next two years so that 2011, 2012, and 2013 crops can use the
phosphorus that was applied in 2011.

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Step 10: Calculate the Manure Application Rate for Crop Years 2012
and 2013
On the basis of step 9, no additional manure should be applied for the next two years after the
2011 multi-year phosphorus application. As indicated by the sample NMP (Table 6.7, Planned
Nutrient Applications), no nutrients from manure are applied in year 2012 or 2013:
Crop Year 2012: Soybean
0 lbs N/acre from manure ≤ 232 lbs N/acre
0 lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre
Crop Year 2013: Corn
0 lbs N/acre from manure ≤ 0 lbs N/acre
0 lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre

Step 11: Calculate the Manure Application Rate for Crop Year 2014
Because no phosphorus will be applied in 2012 and 2013 because of the 3-year phosphorus
application in year 2011, manure nutrients can be applied again in year 2014. As shown in
steps 1–7, the sample NMP indicates that no other sources of nitrogen will be applied in crop year
2014. In steps 1 through 7, the amount of nutrients to be applied from manure was calculated as
follows:
X lbs of N/acre from manure ≤ 232 lbs N/acre
and
X lbs P2O5/acre from manure ≤ 244 lbs P2O5/acre
Manure nutrients can be used to supply 232 lbs of N/acre to the soybean crop as long as the
manure application is in compliance with the medium field risk and does not contain more than
244 lbs of P2O5/acre. As shown in step 7, the NMP indicates that no additional manure will be
applied for crop year 2014. Therefore, the NMP demonstrates compliance with the permit terms
with respect to manure application because
0 tons manure = 0 lbs N/acre
0 lbs N/acre < 232 lbs N/acre
and
0 lbs P2O5/acre < 244 lbs P2O5/acre
Table 6.7, Planned Nutrient Applications in the sample NMP shows that in September of 2014,
20 tons/acre of W Lots Stack #2 manure will be surface applied with a dry box spreader. A soybean
crop is planted in year 2014, and those nutrients are not to supply the nutrient needs of the soybean
crop. That is a fall application (and it is indicated in Table 6.7) that the nutrients are applied to supply
the next spring’s corn crop. Those nutrients should be credited to the next year’s permit cycle.
6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

Putting together all the terms that are applicable to the narrative rate approach:
The methodology is expressed within MMP version 0.29. The permitting authority has
determined that the methodology used by MMP encompasses all the factors of the methodology,
and the plan was developed in accordance with the state’s technical standard. Additional sitespecific permit terms for expressing protocols for land application under the narrative rate
approach include the following:
Fields
available
for land
application
SubField field

Outcome of the assessment
of the potential for nutrient
transport
Crop
year

Total
acres

Bob’s Farm South

2010

8S

2011
2012
2013
2014

79.6

Planned
crops or
other
use

Realistic
annual
yield
goal

Field slope 7%. Manure
Low
Manure shall not be Soybean
applied in excess of
may only be surface
applied to this field when
the nitrogen needs
of the crop
the ground is frozen,
snow covered or saturated
Medium Manure shall not be
Corn
if one of the following
applied in excess of
conditions exists:
two times the crop
Medium phosphorus removed Soybean
1. Where manure storage
with crop harvest
capacity is insufficient
over the period of
and failure to surface
Medium
Corn
the crop rotation
apply creates a risk of an
uncontrolled release of
manure
Medium
Soybean

61
bu/acre

Timing limitations
for a land application

P loss
risk

Allowable manure
application rate

2. On an emergency basis

Subfield

Crop
year

Max lbs N
derived from all
sources

Max lbs P2O5
derived from all
sources

Soybeans = 0 lbs
N/acre

Soybeans = 0 lbs
P2O5/acre

Corn = 210 lbs N/
acre

Corn = 190 lbs
P2O5/acre

195
bu/acre
61
bu/acre
195
bu/acre

Total nitrogen and
phosphorus
recommendations
for each crop on
each field

Soybean
recommendations
232 lbs N/acre
49 lbs P2O5/acre
Corn
recommendations
210 lbs N/acre
73 lbs P2O5/acre

61
bu/acre

Alternative crop
Alternative
crop

Yield goal

Total N
recommendation

Total P2O5
recommendation

Wheat

78 bu/acre

88

41

Alfalfa

4.1 ton/
acre

205

51

2010
2011
8S

2012
2013
2014

6. Protocols for Land Application of Manure Nutrients
6.1. Soil and Plant
Availability of Nutrients

6.2. Using Manure Nutrients

6.3. Standards for Nutrient
Management

6.4. EPA’s CAFO
Requirements for Land
Application

6.5. Protocols for Land
Application

6.6. Permit Terms for Land
Application Protocols
Using a Sample NMP

6.6.3. Additional Site-Specific Terms: Narrative Rate Approach

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NPDES Permit Writers’ Manual for CAFOs

References
Iowa DNR (Department of Natural Resources). year. Manure Management Plan Form. Iowa
Department of Natural Resources, City, IA.
Iowa State University Extension. 2008. Using Manure Nutrients for Crop Production. PMR1033
Iowa State University Extension, Ames, IA.
Kellogg, R.L., C.H. Lander, D.C. Moffitt, and N. Gollehon. 2000. Manure Nutrients Relative to the
Capacity of Cropland and Pastureland to Assimilate Nutrients: Spatial and Temporal Trends for
the United States. U.S. Department of Agriculture, Natural Resources Conservation Service,
Washington, DC.
NRCS, Iowa (Natural Resources Conservation Service, Iowa). 2004. Iowa Technical Note No. 25.
Iowa Phosphorus Index. Natural Resources Conservation Service, Iowa, Des Moines, IA.
NRCS, Iowa (Natural Resources Conservation Service, Iowa). 2008. Natural Resources
Conservation Service, Conservation Practice Standard, Nutrient Management (Ac.) Code 590.
Natural Resources Conservation Service, Iowa, Des Moines, IA.
Osmond, D.L., M.L. Cabrera, S.E. Feagley, G.E. Hardee, C.C. Mitchell, P.A. Moore Jr., R.S.
Mylavarapu, J.L. Oldham, J.C. Stevens, W.O. Thom, F. Walker, and H. Zhang. 2006.
Comparing ratings of the southern phosphorus indices. Journal of Soil and Water
Conservation 61(6):325–337.
USDA-NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service).
1999. Agricultural Waste Management Field Handbook. U.S. Department of Agriculture,
Washington, DC.
USDA-NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service). 2006.
Nutrient Management Conservation Practice Standard 590. U.S. Department of Agriculture,
Washington, DC.
USEPA (U.S. Environmental Protection Agency). 2003. Development Document for the Final
Revisions to the National Pollutant Discharge Elimination System (NPDES) Regulation and the
Effluent Guidelines for Concentrated Animal Feeding Operations (CAFOs). EPA-821-R-03-001.
U.S. Environmental Protection Agency, Washington, DC.

6. Protocols for Land Application of Manure Nutrients

NPDES Permit Writers’ Manual for CAFOs

Endnotes
All terms of the NMP are italicized in this chapter.

1

Notice of proposed changes to the national handbook of conservation practices (including the 590 standard) for the
Natural Resources Conservation Service was published in the Federal Register on January 11, 2011.
(See http://edocket.access.gpo.gov/2011/pdf/2011-373.pdf) Revisions to the 590 conservation standard were finalized
in January 2012 and are available at http://www.nrcs.usda.gov/wps/portal/nrcs/main/national/landuse/crops/npm

2

Land application of manure is often handled differently than land application of industrial waste or biosolids.
40 CFR part 503 subpart B provides information for land application of biosolids to agricultural land. Many states
use similar regulations for other industrial wastes. Those rules often require tracking of many nutrients, metals, and
other potential contaminants. They also usually require crediting for nutrient availability over multiple years. Usually,
they do not require any type of phosphorus risk analysis. Animal waste is typically a much more homogenous and
consistent source of nutrients. Nitrogen or phosphorus is almost always the limiting constituent for determining
manure application rates. When application rates are based on those nutrients, the accumulation of metals in the
soil is rarely a problem. The nutrients in manure are also more readily available than the nutrients in most industrial
wastes. Given those differences, care should be taken when comparing the land application of manures to regulations
on land application of other wastes.

3

The January 2012 revised NRCS 590 conservation standard requires the use of an NRCS approved nitrogen and
phosphorus risk assessment tool. An NRCS approved risk assessment tool meets the technical criteria outline in
the National Instruction Document NI-190-302 (located: http://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/
stelprdb1046435.pdf).

4

Portions of the information in this section are extracted or adapted from NRCS, The Phosphorus Index, A
Phosphorus Assessment Tool (August 1994) at http://www.nrcs.usda.gov/technical/ecs/nutrient/pindex.html.

5

State indices can vary so much in fact, that P-indices should not be used in states other than that for which they
were developed, and risk categories are generally not comparable state to state.

6

An exception is for nitrogen recommendations provided with soil analysis reports. Analytical labs often make
nitrogen recommendations according to the results of the soil analysis. The recommendations consider the yield
goal and the soil nutrient content. Some state technical standards allow use of laboratory recommendations for
nutrient management planning.

7

Note that, because the amount of nutrients to be supplied from manure is not a term under the narrative rate
approach, the operator is not limited to 32 lbs of nitrogen from manure. If the amount of commercial fertilizer is
decreased, more manure could be applied as long as the total amounts of nitrogen and phosphorus applied do not
exceed the term maximum amount of nitrogen and phosphorus to be applied from all sources.

8

6. Protocols for Land Application of Manure Nutrients

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NPDES Permit Writers’ Manual for CAFOs

Appendix
Basic Soil Science
and Soil Fertility

A

NPDES Permit Writers’ Manual for CAFOs

A-1

NPDES Permit Writers’ Manual for CAFOs

Introduction
Understanding the nutritional needs of plants can be quite complex, given the dynamic nature
of plant nutrients in the soil. Nutrients can exist in organic or inorganic forms and in various
phases. They can exist in solution, on mineral surfaces, or be retained in the structural framework
of soils. Environmental conditions affect nutrients’ transformations and movement in the soil,
which determines their availability for plant uptake. In managed systems, understanding those
transformations is essential for maintaining nutrient balances to properly supply a plant’s
nutritional requirements with minimal effect on the environment.

Soil Formation and Basic Morphology
Soil is the layer of unconsolidated material on the immediate surface of the earth that is capable
of supporting plant life. Most soils contain four basic components: mineral particles, water, air,
and organic matter. Organic matter can be further subdivided into roots, living organisms, and
humus (a dark colored, semi-soluble organic substance formed from decomposition of other
soil organic matter). A soil in good condition for plant growth will have a volume composition
of approximately 50 percent solid material and 50 percent pore space. Under ideal moisture
conditions for plants, the soil pore space would also consist of about half air and half water by
volume (Figure A-1).

Figure A-1. Average composition of soil.
(Source: Pidwirny, M. J., Fundamentals of Physical Geography)

Appendix A. Basic Soil Science and Soil Fertility
Soil Formation and Basic Morphology

A-2

NPDES Permit Writers’ Manual for CAFOs

The mass of dry soil per unit of bulk volume, including the airspace, is called the soil bulk density.
Bulk density is an indicator of soil quality. Soils with a high proportion of pore space to solids
have lower bulk densities than those that are more compact and have less pore space. As bulk
density increases, pore space is reduced, which ultimately inhibits root growth. Not only is it
more difficult for roots to penetrate through the soil, fewer pores means less aeration and water
infiltration both of which also deteriorate the conditions necessary for optimum crop growth.
Fine-textured soils such as silt loams, clays, and clay loams generally have lower bulk densities
than sandy soils. Sandy soils typically have less total pore space than finer textured soils. Sandy
soils lack the micro-pore spaces that exist within soil aggregates, which finer textured soils
contain in addition to the macro-pore spaces that exist between soil aggregates (Figure A-2).1
Although finer textured soils have very
low bulk densities, when they become
compacted, the bulk density can be
quite high.
Heavy animal traffic and repeatedly
driving farm equipment over fields
and can compact soils, increasing the
bulk density. Compaction deteriorates
plant growth, and increased bulk
density means a diminished capacity to
infiltrate water and, therefore, greater
surface runoff. It is extremely difficult
to decrease the bulk density of a soil
once it has been compacted. Tillage
practices can initially loosen the soil
surface and improve aeration and
Figure A-2. Soil aggregates, aka micro & macro.
infiltration; however, over long periods
those practices also lead to an overall
increase in soil bulk density. The effects
that different practices can have on increasing soil bulk density should be considered so that they
can be minimized to improve the longevity of the soil, reduce surface runoff and help crops reach
optimum yield potentials.
Soil is largely made up of mineral material from weathered rock (also called parent material),
which is the product of thousands of years of physical processes. Temperature changes, water, ice
and wind abrasions, and plants and animals all act to physically wear down rock and minerals.
Physical weathering exposes greater amounts of surface area that can simultaneously weather
through chemical processes. Many chemical reactions can take place during soil formation.
Acid-producing reactions are one example that is enhanced once a soil begins supporting living
organisms. Carbon dioxide is emitted through respiration and decomposition. Carbon dioxide
dissolves in water held in the soil pore spaces to form carbonic acid, which dissolves minerals.
Physical and chemical weathering will occur simultaneously and enhance each other, greatly
speeding up the soil-forming process.

Appendix A. Basic Soil Science and Soil Fertility
Soil Formation and Basic Morphology

A-3

NPDES Permit Writers’ Manual for CAFOs

The soil-forming process produces distinct visible layers, called horizons, in the soil. The horizons
are defined by the soil’s color, texture, consistency, and structure. Horizons will also vary in
chemical characteristics or composition. Figure A-3 shows the major horizons in a soil profile.
Some soils will have an O (organic) horizon on the surface that consists mainly of plant litter at
various levels of decomposition. The O horizon is unlikely to be identified in cultivated fields
because the layer is easily lost though erosion that can result from years of plowing and tilling.
Horizon A is the surface soil (also called
the topsoil) and is the layer where crops
are planted and grown. Typically, the
layer contains more organic matter
and is coarser than the lower horizons.
The humus in the surface soil imparts
a distinct grayish to dark-brown to
black color to the horizon. Generally,
the darker the color of a soil, the more
humus is present. Horizon A is the zone of
maximum biological activity.
Horizon B is the subsurface soil, which is
also called the subsoil. There is generally
more clay, which makes the horizon
finer-grained than the surface horizon.
Horizon B’s color is usually brighter,
ranging from red to brown to yellow. The
layer generally accumulates all or most of
the silicates, clay, iron, and aluminum in
the soil.
Horizon C is formed in the parent material
and has acquired some characteristics of
the subsoil. The parent material can be
alluvium, loess, colluvium,2 or bedrock.
If formed in bedrock, the layer will
sometimes look like weathered rock, but
it is soft enough to be dug into and will
crumble easily.

Figure A-3. The major horizons in a soil profile.
(Source: Illinois Central Core)

The R horizon, if present, consists of unweathered bedrock.

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Soil Properties
The properties of a soil result from the environmental factors and conditions that shaped the soil.
The following characteristics are important factors that determine a soil’s suitability for use and
its management needs.

Organic Matter
Organic matter in soil is derived from decomposed plant and animal material. The amount of
organic matter depends on the type of plants that are growing in the soil, how long the plants
have been growing, and the water content or moisture in the soil. Humus is the most reactive and
important component of soil organic matter.
An adequate level of humus provides soil with a number of benefits:
▶ Increased ability to hold and store moisture.
▶ Helps maintain porosity in fine-textured soils.
▶ Reduces leaching of soluble nutrients to lower soil layers.
▶ Important source of carbon and nitrogen (N) for plants.
▶ Improves soil structure for plant growth.
▶ Decreases erosion losses.

Texture
Texture refers to the fineness or coarseness of the mineral particles in the soil and is determined
by the relative amounts of different sized mineral particles in the soil. Particles are normally
grouped into three main classes: sand, silt, and clay (Table A-1).
Table A-1. Soil classification by particle size
Classification

Soil particle size

Sand

0.05 to 2 mm

Silt

0.002 to 0.05 mm

Clay

< 0.002 mm

Mineral particles that are larger than 2 mm in diameter are considered coarse fragments. Mineral
particles that range from 0.05 mm to 2 mm in diameter are called sand. Sand feels rough when
rubbed between the thumb and fingers. Soil particles between 0.002 mm to 0.05 mm in diameter
are classified as silt. Dry silt feels smooth and silky and retains an imprint when pressed. Wet silt
remains smooth and does not become slick or sticky. Clay is the finest sized particle, with each

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particle smaller than 0.002 mm in diameter. When dry, clay feels very smooth. When wet, clay
becomes slick and sticky and holds its form when shaped.
The proportion of sand, silt, and clay form the basis for 12 primary classes of soil texture (Figure A-4
and Table A-2). The texture of a soil affects the movement of air and water, as well as plant root
penetration. However, most importantly, the texture of a soil determines the amount of surface
area available. The surface of a mineral is where water, nutrients, chemicals, microorganisms, and
charges are held and released. That ultimately determines the soil’s water-holding capacity and
fertility. Coarse and sandy soils allow for more rapid infiltration rates for water as opposed to more
fine-textured or clay soils. Sandy soils are also easier to till. Sandy soils are suited for producing
specialty crops such as vegetables, tobacco, and peanuts. Fine‑textured soils hold more water and

Figure A-4. Soil textural triangle. (Source: USDA/NRCS)

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plant nutrients and require less frequent nutrient applications. Moisture has a significant effect
on the workability of fine soils. Such soils can form puddles after a rain and can develop a crust.
Fine-textured soils are best suited for producing corn, small grains, hay, and forages.
Table A-2. Soil texture classes
Texture classes of soilsa
Common names

Texture

Class names

Sandy soils

Coarse

Sandy, loamy sands

Loamy soils

Moderately coarse

Sandy loam, loam

Medium

Silt loam, silt, clay loam

Moderately fine

Sandy clay loam, silty clay loam

Fine

Sandy clay, silty clay, clay

Clayey soils
a.

Adapted from Smith 1990

Aggregation and Structure
The cementing or binding together of several soil particles into a secondary unit is called soil
aggregation. The soil particles are arranged or grouped together to form structural pieces
(building blocks) called peds or aggregates, in various shapes and sizes. The arrangement of the
aggregates determines the soil’s structure (Figure A-5).
Structure is an important soil characteristic because good structure allows favorable movement
of air and water and allows and encourages extensive root development.
The formation of aggregates and good structure of the surface soil is promoted by a proper
supply of organic matter, adequate lime, and working or tilling the soil during correct moisture
conditions. On the other hand, structure is weakened or destroyed when organic matter is
depleted, when inadequate lime is used, and when the soil is tilled or worked with too much or
too little moisture in the soil.

Color
The color of a soil has little influence on a soil’s function; however, it tells a great deal about the
soil. Soil colors are often a result of the various oxidation states of the minerals present. Brighter
colors such as yellow and reds are an indication of iron oxides. The brighter colors suggest good
drainage and aeration. Grayish soils can indicate iron reduction caused by permanently saturated
soil. Soils with mottled colors of various shades of yellow, brown, and gray are indicative of a
fluctuating aerobic and anaerobic environment. Aside from iron, other minerals that contribute
to soil color are manganese oxide, glauconite, and carbonates. Additionally, very dark browns and
black soil colors can be an indication of high levels of organic matter.

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Granular: Resembles cookie
crumbs and is usually less than
0.5 cm in diameter. Commonly
found in surface horizons where
roots have been growing.

Platy: Thin, flat plates of soil that
lie horizontally. Usually found in
compacted soil.

Single Grained: Soil is broken into
individual particles that do not stick
together. Always accompanies a
loose consistence. Commonly found
in sandy soils.

Source: A-5.
Soil Science
Education
Home Page
Figure
Examples
of soil structure.
(Source: Soil Science Education home page)

Retention/Water-Holding Capacity
The amount of water retained in a soil is dependent on the interaction of soil texture, bulk
density, and aggregation. The term field capacity defines the amount of water remaining in a soil
after downward gravitational flow has stopped, and it is expressed as a percent by weight. The
permanent wilting percentage represents the amount of water in soil after plants are permanently
wilted. Water is still in the soil, but it is held so tightly that it is unavailable for plant use. The
difference between field capacity and the wilting point is the plant-available water (Figure A-6).
Irrigation water is generally applied when the soil moisture is depleted by 40 to 60 percent of field
capacity. Irrigation water is applied to bring the soil moisture back to near field capacity.
Sandy soils hold little water because their large pore spaces allow water to drain freely. While
clay soils have greater water-holding capacities because of their small pore spaces, they also hold
water more tightly than sandy soils, making a certain amount of water unavailable to plants. The
amount of organic matter and stoniness in soils improves the available water capacity for plant
use. Coarser soils tend to have the lowest plant available water capacity, while medium-textured
soils tend to have the highest. Decreasing the bulk density of soils reduces water-holding capacity.

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Figure A-6. Plant available water and drainable water in
relation to field capacity and wilting point.
(Source: University of Minnesota)

Drainage
Soil drainage is defined as the rate and extent of water removal. That includes water movement
across the surface and downward through the soil. Topography is a very important factor in soil
drainage. Other factors that affect drainage include the soil layers’ texture and soil structure.
Poor drainage is indicated by a mottled gray soil color, constantly wet soil, or water sitting on the
soil surface for a long time after rain or irrigation. If drainage is poor, plant roots are deprived
of oxygen. Thus, adequate drainage is essential to good plant growth. Conversely, excessively
drained soils, such as very sandy soils or those on steep slopes, tend to hold too little water for
normal plant growth.

Cation Exchange Capacity
Soil materials have a net surface charge, usually negative, that allows them to hold and retain ions
(i.e., nutrients) against leaching. The net negative charge of a soil is largely attributed to the clay
and organic matter in the soil and will naturally attract positively charged nutrients and repel
negatively charged nutrients. That explains why cations, the positively charged nutrients (such
as ammonium (NH3+)), remain in the soil while anions, the negatively charged nutrients (such as
nitrate (NO3-)), are repelled and easily leached out of the soil.
The cation exchange capacity (CEC) is a measure of the soil’s ability to retain cations and,
therefore, is indicative of the soil’s fertility. In addition to clay and organic matter, pH has an effect
on CEC. Increasing soil pH increases its CEC, activating more ion exchange sites.

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Soils with low CEC can have one or more of the following characteristics:
▶ High sand and low clay content.
▶ Low organic matter content.
▶ Low water-holding capacity.
▶ Low pH value.
▶ Lightly buffered and cannot easily resist changes in pH or other chemical changes.
▶ Nutrients are leached very easily.
▶ Productivity can be low.
▶ Certain types of clay such as kaolinite will have a much lower CEC than a
montmorillonite or vermiculite (high shrink and swell clays).
Soils with a higher CEC can have one or more of the following characteristics:
▶ Low sand and high clay content.
▶ Moderate to high organic matter content.
▶ High water-holding capacity.
▶ Highly buffered and resist changes in pH or other chemical changes.
▶ Nutrients are retained and leaching losses reduced.
A soil’s CEC directly affects the amount of fertilizer that should be used and the frequency with
which it should be applied.

Soil Fertility
Soil fertility is the ability of a soil to provide nutrients for plant growth (Table A-3). Many factors
affect the availability of elements in soil, including the form of the element found in the soil, pH,
soil aeration, soil compaction, soil temperature, and soil moisture. As described, the ability of a
soil to retain nutrients is related to its CEC. Many of the important plant nutrients are cations,
which are retained by the soil’s negative charge. Those include ammonium (NH4+), calcium (Ca2+),
potassium (K+), sodium (Na2+), aluminum (Al3+), hydrogen (H+), and magnesium (Mg2+). As the
CEC increases, the soil’s ability to retain and provide nutrients to plants increases. Therefore,
the fertility and productivity of a soil can be greatly influenced by the CEC. Negatively charged
ions, or anions, are leached than positively charged ions. For example, NO3- is not retained in the
soil profile because of its negative charge. An exception occurs with phosphorus (P). Although
it exists in the anionic form, the properties of phosphate anions allow them to (1) react with
other minerals in the soil and form low-solubility compounds that are unavailable to the plant
and (2) to become fixed on and in available sites of clay particles through a process known as

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phosphorus fixation. Thus, phosphorus leaching is limited unless soil concentrations become
very high or in sandy soils because of limited fixation sites.
Table A-3. Essential plant nutrients
Plant-available forms of essential elements
Primary plant nutrients
Nitrogen

NH4+, NO3-

Phosphorus

HPO42-, H2PO4-

Potassium

K+

Secondary plant nutrients
Calcium

Ca2+

Magnesium

Mg2+

Sulfur

SO42-

Carbon

CO2

Hydrogen

H+, OH-

Soil pH affects plant nutrient availability because pH greatly influences the solubility of certain
elements. Most crops grow best in slightly acidic soils (pH 6.0 to 6.5). Acidification is a natural
and continuous process in many soils. Through chemical weathering, cations are released from
parent materials and become available on the exchange complex of a clay particle. Soils become
acidic when the cations are displaced by acid ions, mostly H+ and Al3+. Acid ions are prevalent in
the soil because of other ongoing chemical processes in the soil that release them. When exposed
to water, the non-acidic cations (K+, Ca2+, and Mg2+) and anions are leached from the soil profile,
leaving the exchange complex and soil solution acidic. In areas with high annual rainfall, soils
tend to be acidic because of the increased leaching conditions. For that reason, soils in Eastern
states are generally more acidic than those in the Midwest and Western United States.
The working of ground limestone into the soil to raise soil pH is referred to as liming. The
benefits of liming are both direct and indirect. Some direct benefits include the reduction of
Al3+ and Mn2+ solubility (both ions are toxic to most plants unless at very low concentrations),
and the application of Ca2+ and/or Mg2+, both of which are plant nutrients. Indirect benefits
include increased microbial activity and the increased Ca2+ levels in the soil can improve the soil
structure. The benefits of liming are generally expected to last for at least 5 and commonly up to
10 years. While liming has many beneficial effects, over liming can easily induce micronutrient
deficiencies in many crops adapted to low or moderate pH conditions.
For a plant to take up nutrients, the nutrient must exist in the soil solution (water-filled pore space)
and be in a soluble form. A large amount of nutrients are stored in the solid framework (mineral
and organic material) of a soil; however, the nutrients are released slowly to the soil solu­t ion

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through chemical and biochemical processes. The soil solution usually holds insufficient quantities of nutrients for plant’s nutritional needs. The larger particles (sand, silt, large clay particles,
and organic matter), tightly entrap and retain certain nutrient species making them available very
slowly over time. Within the colloidal size fraction, nutrients are exposed to a greater surface area
and broken down faster, but they are still entrapped and, thus, are only slightly more available.
Nutrient ions are also adsorbed to mineral surfaces, in what is considered an exchangeable form,
but the nutrients are also only moderately available. It is only when they reach the soil solution
that nutrients are free and available for plant uptake and considered plant available.
In addition nutrients being plant available, nutrients must be at the root surface for uptake. If
nutrients are not in direct contact with the root, they must move by mass flow or diffusion. Root
uptake of nutrients is an active metabolic process. Therefore, even if adequate plant-available
nutrients are present, factors that deter flow and root metabolism, such as soil compaction, cold
temperatures, lack of water or oxygen, can inhibit plant uptake of nutrients.

Forms and Fate of Nitrogen
Nitrogen is an essential part of amino acids, the building blocks for proteins, making it an
important plant nutrient. In the soil, it exists in both organic (proteins, amino acids, urea, in
living organisms and decaying plant and animal tissues) and inorganic forms [ammonium
(NH4+), nitrite (NO2-), nitrate (NO3-), and ammonia (NH3(gas))]. The majority of nitrogen in the soils
is in an organic form (95 to 99 percent as amine groups in proteins), which is largely unavailable
for plant uptake. Figure A-7 illustrates the processes responsible for converting nitrogen into plant
available forms.
Microbes break down organic compounds releasing ammonium ions through a process called
mineralization. Mineralization occurs as a result of decomposition. The factors that control
decomposition control the rate of mineralization and, therefore, the rate at which plant available
nitrogen is released to soil. Factors controlling decomposition include soil conditions that
encourage microbial growth and the carbon:nitrogen (C:N) ratio of the compound that is being
degraded. Adequate soil moisture and aeration, near-neutral soil pH, and warm soil temperatures
are conditions that are favorable to a broad range of organisms.
Microbes need carbon, but they also require nitrogen for building cells and extracting energy.
The C:N ratio of the compound being decomposed is a critical factor in determining if nitrogen is
utilized by the microbes for energy and depleted from the soil or supplied to the plant available
nitrogen pool in the soil. When materials with a high C:N ratio, such as corn stalks (C:N ratio
is typically 55:1) are added to soil, microorganisms begin to degrade the compound as a food
source. Given the limited amount of nitrogen in the source itself, the microbes will scavenge the
soil for available nitrogen, which is necessary for decomposition. In such situations, the soil can
be depleted of plant available nitrogen. On the other hand, when an organic compound with a low
C:N ratio, such as alfalfa hay (C:N ratio is typically 13:1) is added to soil, there is sufficient nitrogen
in the compound itself for decomposition. The microbes do not need to use nitrogen from the

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Figure A-7. The Nitrogen Cycle.

soil. Rather, decomposition of the material can release plant available nitrogen from the organic
compound to the soil.
As mineralization occurs, if ammonium is released to the soil, it can be directly absorbed by a
plant or it can be oxidized to nitrate and then absorbed. Because soil systems often are aerobic,
ammonium does not typically persist in the soil in large quantities. Ammonium is a positively
charged ion, which means, if it is present in a soil, it can be retained by the negatively charged soil
particles on a soil’s exchange complex. As previously mentioned, nutrients held on the mineral
exchange complex are moderately plant available because, while they are retained on the mineral
surface, they can be displaced by competing ions to the soil solution. Ammonium can also
become fixed within the crystal structure of certain types of clay particles because of its size and
the arrangement of the specific clay particles. Fixed ammonium is only slowly released to the soil
solution and would not be a sufficient source of nitrogen for plants.

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When manure is land applied as an organic compound, only a small fraction of the nitrogen
might be soluble as ammonium and plant available. However, a larger portion of that nitrogen
is mineralized by microbes and slowly released over many years. Nitrogen mineralization
rates of the organic nitrogen present in the initial land application vary depending on various
environmental factors such as soil type, the manure source, and climate. For example, cattle
manure mixed with bedding that has been stored under cover will have approximately 60 percent
of the organic nitrogen fraction mineralized in the year of application; 6 percent in the second
year, and 2 percent in the third year. For many types of manure, 1 to 4 percent of organic nitrogen
is still being released 4 years after the initial application. Therefore, calculations to determine
annual land applications of nitrogen should account for released forms of nitrogen from previous
organic nitrogen applications.
As nitrogen-containing organic compounds such as manure and fertilizers are broken down,
ammonia can be released. Ammonia is most commonly found as a gas and is released from a soil
system through a process called volatilization. Volatilization occurs at the liquid air interfaces
and is controlled by the pH and water content of the soils, which drive nitrogen either into or out
of the soil. The loss of ammonia to the atmosphere is driven by high level pH soils. The importance
of incorporating manures into soils is to minimize the contact area between the manure and the
ambient air to reduce ammonia volatilization. Soils and plants have the ability to sorb ammonia
from the atmosphere, but fertilizer recommendations do not consider atmospheric nitrogen
sources. As a result, areas that are exposed to high atmospheric ammonia concentrations (such as
intensive livestock operations) could be having fertilizers applied at rates in excess of plants’ needs.
Nitrate is another plant available form of nitrogen that can enter the soil system through
atmospheric deposition, commercial fertilizers, and transformation of ammonium as mentioned
above. Ammonium is oxidized to nitrite, which is quickly oxidized to nitrate by nitrifying bacteria
as long as favorable soil conditions exist for the bacteria to survive. Nitrite is also plant available,
but it can be toxic to plants and rarely persists in the soil in significant concentrations. As
opposed to ammonium, nitrate is a negatively charged ion that is not adsorbed to the negatively
charged soil mineral surfaces. Therefore, nitrate is readily available to plants, but if excess nitrate
persists in the soil solution, the negatively charged nutrient is repelled by the soil surfaces and lost
to groundwater through leaching. Factors that contribute to nitrogen leaching or runoff include
over-application of nitrogen as fertilizers or manure particularly on sandy or coarse-textured
soils; improperly timed applications of nitrogen, poorly designed or nonexistent soil conservation
measures; and periods of exceptionally heavy rainfall.
Anaerobic bacteria can also reduce nitrate to nitrogen gas through a process called
denitrification. Denitrification is a series of bacteria driven reduction reactions that reduce nitrate
ultimately to nitrogen gas. Because denitrification is a reduction reaction, it requires an anaerobic
environment, such as saturated soils. Only when soil oxygen levels are low enough, typically in
waterlogged or poorly drained soils, will nitrate be fully reduced resulting in the formation of
nitrogen gas. When oxygen levels fluctuate, as they commonly do in the field, nitrate will not be
fully reduced and nitric oxide (NO) and nitrous oxide (N2O) can be released to the atmosphere
because those are intermediate by-products.

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Forms and Fate of Phosphorus
Phosphorus is an important plant nutrient because it is an essential component of deoxyribo­
nucleic acid (DNA), ribonucleic acid (RNA), and the nucleotide adenosine 5’-triphosphate
(ATP), which are necessary for intracellular energy transfer. Unlike nitrogen, gaseous forms of
phosphorus seldom exist and are often not considered in the phosphorus cycle (Figure A-8).
Organic phosphorus usually occurs in microbial biomass and organic matter compounds.
Inorganic phosphorus commonly appears in the form of phosphates (HPO4-2 and H2PO4-). Relative
to other nutrients, phosphorus in soil solution is found in very low concentrations (0.001 to
1 mg/L) that rarely exceed 0.01 percent of total soil phosphorus.
When phosphate ions are added to a soil, they are quickly (within hours) removed from solution
to form phosphorus containing compounds with very low solubility. Phosphate most commonly
forms compounds with either calcium or iron and aluminum (sometimes manganese). Initially,
some ions are retained on the exchange complex, which makes them moderately plant available
but with time, they undergo sequential reactions that continually decrease their solubility.

Figure A-8. The Phosphorus Cycle.

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Such reactions result in phosphorus permanently bonding to the calcium or aluminum/iron/
manganese ions, becoming buried under products from additional precipitation reactions.
Those reactions can also entrap phosphorus within the calcium or iron/aluminum/manganese
particles. That is regarded as phosphorus fixation and it is not easily reversible.
The capacity for soils to fix phosphorus depends on a number of soil factors including the mineral
type, pH, and amount of organic matter. Phosphate ions are negatively charged; therefore, the
minerals sorbing and fixing the ions must be positively charged. Certain types of minerals have
a greater capacity for sorbing anions than others. The pH of the soil affects the solubility of the
calcium and iron and aluminum phosphate compounds with the greatest fixation occurring at
low and high pH values. Organic matter and by-products from its decomposition compete with
phosphate ions for adsorption sites on mineral surfaces; therefore, soils with low organic matter
concentra­t ions tend to fix more phosphorus, making less available to plants. Because fixation
depends on available mineral surface area and sorption sites, soils have a finite capacity to fix
phosphorus.
Additions of fertilizers and manures typically allow for only 10 to 15 percent of added phospho­
rus to be taken up by plants because of that fixation capacity. Therefore, during the early and
mid‑20th century, farmers applied phosphorus in quantities far in excess of the plants’ nutritional
needs. In addition, manure has historically been applied at rates to meet plant nitrogen require­
ments, which can supply 2 to 4 times the phosphorus requirement. What was not removed in the
harvest could accumulate in the soil in an insoluble, unavailable form. That became common
practice and over the years, many fertilized, cultivated soils have reached their phosphorus
fixation capacity. Note that that was not the case everywhere. In many developing countries
where fertilizer is seldom used, phosphorus is often the limiting nutrient in food-crop production.
If not taken up by plants, phosphorus can be lost with surface runoff as dissolved phosphorus
(if not incorporated into a soil) or it can be lost with soil particles through erosion or colloid
leaching if sorbed to mineral surfaces. Soil particles containing fixed phosphorus that are lost
through erosion might not appear to degrade water quality because of phosphorus fixation.
However, in prolonged anaerobic environments (i.e., river beds) iron that is binding phosphorus
will be reduced. While oxidized iron is insoluble, reduced iron is soluble allowing for the bound
phosphate to be released into solution, contributing to water quality problems like eutrophication.

Water Quality
Water pollution from cropland is controlled in large part by the hydrologic cycle. Precipitation
and irrigation add water, which, once at the soil surface, infiltrate, pond, or run off. Two types
of losses from soils that affect water quality are (1) percolation or drainage, and (2) runoff.
Percolation results in the loss of soluble elements (leaching), thus depleting soils of certain
nutrients. Runoff losses generally include water and appreciable amounts of soil (erosion).
Two prime reasons raise concern over the loss of essential elements by leaching and erosion.
First is the obvious concern for keeping nutrients in the soil so that they are available to crops. A

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second and equally significant reason is to keep the nutrients out of streams, rivers, and lakes.
Nitrate contamination of ground and surface waters can cause serious environmental damage.
Nitrates in drinking water are toxic because they reduce the capacity for blood to carry oxygen.
That can be lethal to human infants and can alter normal body functioning in adults. Some
underground sources of drinking water have become sufficiently high in nitrate causing health
concerns for humans. Likewise, surface runoff waters from heavily fertilized lands can contain
levels of nitrate toxic to livestock. While phosphorus is not toxic, it can degrade water quality
if lost from a soil system in significant quantities. Excessive growth of algae and other aquatic
species takes place in water overly enriched with nitrogen and phosphorus. That process, called
eutrophication, depletes the water of its oxygen, thus harming fish, other aquatic species, and
ultimately most life in the waterbody.

Infiltration, Percolation, and Leaching
As water enters a soil (infiltration) and moves down through the soil profile (percolation) it carries
dissolved nutrients with it (leaching). Leaching losses occur when the amount of rainfall or
irrigation water entering a soil exceeds the soil’s ability to store it. The amount and rate of nutrient
losses are influenced by the amount of rainfall or irrigation, the topography of the landscape, the
amount of evaporation, the soil type, and the crop cover.
Soil properties have an effect on nutrient leaching losses. The physical properties of sand, silt, and
clay, and the relative proportions of each have direct bearing on nutrient retention. As discussed,
coarse soils (soils with a high percentage of sand) generally permit greater nutrient loss than do
finer textured soils (soils with higher percentage of silt and clay). Organic matter content and type
and amount of clay have significant influence on retention and nutrient storage and exchange.
The loss of nutrients through leaching is also influenced by climatic factors. In regions where
water percolation is high, the potential for leaching is also high. Such conditions exist in the
United States in the humid east and in the heavily irrigated sections of the west. In non-irrigated,
semiarid areas, less nutrient leaching occurs because less water is added to the soil to contribute
to the leaching process.
The proportion of rain or irrigation water entering the soil is enhanced by practices that keep
the soil surface covered (e.g., with vegetation or mulch) to protect it from the beating action of
rain drops that breaks down soil surface structure, decreasing porosity. Rain on bare soil also
displaces soil particles that are easily transported by surface runoff.
Numerous best management practices are available to encourage residue management and
to minimize negative consequences of soil tillage. Excessive tillage that destroys the surface
roughness should be avoided. Tillage across the slope, leaving small ridges, encourages water
infiltration. Likewise, terraces can help control the erosive potential of water movement and
increase infiltration into the soil.

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Runoff and Erosion
A primary principle of soil water management is to encourage water movement into rather than
off the soil. The more water runs off the surface, the less infiltrates into the soil. Maintaining good
soil structure is critical to reducing runoff; excess water that cannot infiltrate the soil accumulates
on the surface and flows downgrade displacing surface soil particles along the way (erosion). Soil
erosion damages productive soils and can increase nutrient transport to streams and lakes.
Two steps are recognized in the erosion process—the detachment or loosening influence and
transportation by floating, rolling, dragging, and splashing. Freezing and thawing, flowing
water, and rain are the major detaching agents. Those actions displace soil particles that are
easily transported by surface runoff. Raindrop splash and especially running water facilitate the
transport of loosened soil.
Following detachment, three types of water erosion are recognized: sheet, rill, and gully. In
sheet erosion, soil is removed more or less uniformly from every part of the slope. However, sheet
erosion is often accompanied by tiny channels (rills) irregularly dispersed, especially on bare
land newly planted or fallow. That is called rill erosion. The rills can be obliterated by tillage, but
the damage is already done—the soil quality in the field is diminished.
Where the volume of runoff water is further concentrated, downward cutting forms larger
channels or gullies. That is called gully erosion. The gullies are obstacles to tillage and cannot be
removed by ordinary tillage practices. While all types can be serious, the losses from sheet and
rill erosion, although less noticeable, are responsible for most of the field soil deterioration.
The quantity of nutrients lost from the soil by erosion can be quite high. Such losses can be
counterbalanced only in part by adding fertilizers; even still soils that are severely eroded
might not respond well to fertilization. Much of the nitrogen and phosphorus lost is in eroded
sediments, which include soil organic matter and finer particles.

Revised Universal Soil Loss Equation Version 23
The Revised Universal Soil Loss Equation, Version 2 (RUSLE2), is designed to predict the longterm average rate of soil loss and guide conservationists on proper cropping, management, and
conservation practices for a field or management unit. RUSLE2 cannot be applied to a specific
storm or a specific year. Agricultural research coupled with centuries of farmers’ experience has
identified the major factors affecting erosion.
RUSLE2 is a computer model that uses a detailed mathematical approach for integrating multiple
equations that describe how factors such as plant yield, vegetative canopy and rooting patterns,
surface roughness, mechanical soil disturbance, amount of biomass on surface, and others affect
soil erosion. The basic structure of the RUSLE2 equation is

A = RKLSCP

Appendix A. Basic Soil Science and Soil Fertility
Runoff and Erosion

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NPDES Permit Writers’ Manual for CAFOs

where
A = predicted average annual soil loss from rill and inter rill erosion caused by rainfall and
its associated overland flow expressed in tons/acre/year.
R = climatic erosivity.
K = soil erodibility measured under a standard condition.
L = slope length.
S = slope steepness.
C = cover and management.
P = support practices (erosion control).
RUSLE2’s predicted soil losses can be compared with soil loss tolerances (T) to provide guidelines
for effective erosion control.

Soil Loss Tolerance
Soil loss tolerance (T) is the maximum amount of soil loss in tons per acre per
year that can be tolerated and still permit a high level of crop productivity to be
sustained economically and indefinitely.
A Natural Resources Conservation Service conservation plan is essentially a set
of conservation practices that are designed to work in an integrated manner to
accomplish an identified level of resource treatment. Developing a conservation
plan involves determining the baseline erosion and other associated losses and
evaluating the practices that would meet T.

RUSLE2’s user interface allows a user to select from its database values to describe site-specific
field conditions for climate, soil, topography, and land use. A brief description of each factor and
the extent of its influence on soil erosion follows:
Rainfall erosivity, the R factor, is the most important climatic variable used by RUSLE2.
Erosivity is related to rainfall amount and intensity, with the latter generally being more
influential. A high annual precipitation received in a number of gentle rains can cause
little erosion, whereas a lower yearly rainfall descending in a few torrential downpours
can result in severe erosion. Temperature is also a key variable as rain and temperature
affect the longevity of materials like crop residue and mulch that can prevent erosion.
RUSLE2 associates erosivity, precipitation, and temperature values with the location
chosen by the user.
The soil erodibility factor, K, indicates the inherent erodibility of a soil. The two most
significant and closely related soil characteristics affecting erosion are infiltration capacity
and structural stability. The infiltration capacity is influenced greatly by structural

Appendix A. Basic Soil Science and Soil Fertility
Runoff and Erosion

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NPDES Permit Writers’ Manual for CAFOs

stability, especially in the upper soil horizons. In addition, organic matter content, soil
texture, the kind and amount of swelling clays, soil depth, tendency to form a surface crust,
and the presence of impervious soil layers all influence the infiltration capacity.
The stability of soil aggregates affects the extent of erosion damage in another way.
Resistance of surface granules to the beating action of rain saves soil even though runoff
does occur. The granule stability of some tropical clay soils accounts for the resistance
of those soils to the action of torrential rains. Downpours of a similar magnitude on
temperate region clays would be disastrous.
Values used by RUSLE2 for soil erodibility have been determined for most cropland and
similar soils across the United States by the U.S. Department of Agriculture–Natural
Resources Conservation Service. The user typically selects a soil-map unit name from a list
of soils in the RUSLE2 database.
Site-specific values are entered for the topographic factor (LS), which reflects the influence
of slope length, steepness, and shape characteristics. The greater the steepness of slope,
other conditions being equal, the greater the erosion, partly because more water is likely to
run off but also because of increased velocity of water flow. The length of the slope or flow
path is important because it is directly proportional to the concentration of the flooding
water.
Land use is the most important factor affecting rill and interrill erosion because it can be
easily changed to reduce erosion. RUSLE2’s cover-management (cultural) practices and
support practices data are used to describe land use.
Soil detachment and erosive forces can be affected by cover-management practices.
The cover and management factor, C, indicates the influence of cropping systems and
management variables on soil loss. C is the factor over which the farmer has the most
control. The type of crop, yield level, and tillage system used are important features to
consider when land is used for crops. Forests and grass provide the best natural protection
known for soil and are about equal in their effectiveness, but forage crops, both legumes
and grasses, are next in protective ability because of their relatively dense cover. Small
grains such as wheat and oats are intermediate and offer considerable obstruction to
surface wash. Row crops such as corn and soybeans offer relatively little cover during the
early growth stages and thereby encourage erosion. Most subject to erosion are fallowed
areas where no crop is grown and all the residues have been incorporated into the soil. The
marked differences among crops in their ability to maintain soil cover emphasize the value
of appropriate crop rotation to reduce soil erosion.
RUSLE2 stores the description of any cover-management practice within its database and
allows for selection of the practice that best fits site-specific field conditions. Key variables
like yield level or mulch application can be changed so that the practice stored in RUSLE2
more accurately reflects the field conditions.

Appendix A. Basic Soil Science and Soil Fertility
Runoff and Erosion

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The support practice factor, P, reflects the benefits of contouring, strip cropping, terraces,
diversions, small impoundments and other supporting factors. Such support practices
reduce erosion primarily by reducing the erosivity of surface runoff. P is the ratio of soil
loss with a given support practice to the corresponding loss when crop culture is up and
down the slope. Like cover-management practices, support practices are selected from the
RUSLE2 database and site-specific information such as the location of a practice is entered
as required.

References
Brady, N.C., and R.R. Weil. 2002. The Nature and Properties of Soils. 13th ed. Pearson Education,
Upper Saddle River, NJ.
Smith, R.L., and T.M. Smith. 1990. Ecology and Field Biology. Pearson Education, Upper Saddle
River, NJ.
USDA-NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service). 2011.
National Soil Survey Handbook, title 430-VI. .
Accessed November 11, 2011.

Endnotes
Soil aggregrates – Groups of soil particles that bind to each other more strongly than to adjacent particles. The space
between the aggregates provide pore space for retention and exchange of air and water.
(Definition from USDA: http://soils.usda.gov/sqi/publications/files/sq_eig_1.pdf.)

1

Alluvium – A general term for all detrital material deposited or in transit by streams, including gravel, sand, silt,
clay, and all variations and mixtures of these. Unless otherwise noted, alluvium is unconsolidated.
Loess – Material transported and deposited by wined and consisting of predominantly silt-sized particles.
Colluvium – A deposit of rock fragments and soil material accumulated at the base of steep slopes as a result of
gravitational action (from Brady and Weil 2002).

2

Adapted from USDA-NRCS 2011.

3

Appendix A. Basic Soil Science and Soil Fertility
Runoff and Erosion

NPDES Permit Writers’ Manual for CAFOs

Appendix

B

Example Letters to
Owners/Operators After
a Site Visit
Example Letter in Follow-up to an Inspection:
Facility Not Designated as a CAFO. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1
Example Letter in Follow-up to an Inspection:
Facility Designated as a CAFO. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-3

NPDES Permit Writers’ Manual for CAFOs

B-1

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Example Letter in Follow-up to an Inspection:
Facility Not Designated as a CAFO

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B-2

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Example Letter in Follow-up to an Inspection:
Facility Designated as a CAFO

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NPDES Permit Writers’ Manual for CAFOs

B-3

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Compliance Assistance Resources
If you operate a small business as defined by the Small Business Administration (defined at
13 CFR 121.201; in most cases, this means a business with 500 or fewer employees), you may find
the following information helpful.
The U.S. Environmental Protection Agency (EPA) and the U.S. Small Business Administration
(SBA) offer small businesses a wide variety of compliance assistance resources and tools designed
to help small businesses comply with federal and state environmental laws. These resources can
help businesses understand their obligations, improve compliance and find cost-effective ways to
comply through the use of pollution prevention and other innovative technologies.
We encourage you to take advantage of these tools to improve your understanding of and
compliance with environmental regulations and avoid the need for future enforcement actions.
Please note that any decision to seek compliance assistance at this time does not relieve you
of your obligation to respond to an EPA request, administrative or civil complaint in a timely
manner, does not create any new rights or defenses, and will not affect EPA’s decision to pursue
this enforcement action.
Dissemination of this information sheet does not constitute an admission or determination
by EPA that your business organization is a small entity as defined by the Small Business
Enforcement and Fairness Act (SBREFA) or related provisions nor does it create any new rights or
defenses under law.

Web sites
EPA offers a great deal of compliance assistance information and materials for small businesses
on the following Web sites:
www.epa.gov

EPA’s Home Page

www.smallbiz-enviroweb.org

Small Business Environmental Home Page

www.smallbiz-enviroweb.org/contacts/sbosbeap.aspx

Small Business Environmental Assistance
Program State Contacts

www.epa.gov/smallbusiness

Small Business Gateway

www.epa.gov/smallbusiness/help.htm

Small Business Assistance, Help, and Training
Web Page

www.epa.gov/compliance/incentives/smallbusiness/

Small Business Compliance and Enforcement

www.epa.gov/compliance/assistance/index.html

Compliance Assistance Home Page

www.epa.gov/oecaagct/tsma.html

EPA Ag Center Small Farm/Small Business
Web Page

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State Agencies
Many state agencies have established compliance assistance programs that provide on-site as
well as other types of assistance. Please contact your local state environmental agency for more
information.

Agriculture Compliance Assistance Center
EPA has established national compliance assistance centers, in partnership with industry,
academic institutions, and other federal and state agencies, that provide assistance services in
sectors heavily populated with small businesses, including agriculture.
▶ Agriculture Compliance Assistance Center: www.epa.gov/agriculture
▶ National Agriculture Center: 1-888-663-2155 or www.epa.gov/agriculture/agctr.html

Hotlines
EPA sponsors more than 50 hotlines and clearinghouses that provide free and convenient avenues
to obtain assistance with environmental requirements. EPA’s Small Business Ombudsman
Hotline can provide you with a list of all the hotlines and assist you with determining which
hotline will best meet your needs. Key hotlines that may be of interest to you include:
▶ EPA’s Small Business Ombudsman................................ (800) 368-5888
▶ Superfund and EPCRA Call Center................................ (800) 424-9346
▶ Safe Drinking Water Hotline...........................................(800) 426-4791

Small Business Compliance Policy
EPA’s Small Business Compliance Policy is intended to promote environmental compliance
among small businesses by providing incentives such as penalty waivers and reductions for
participation in compliance assistance programs, and encouraging voluntary disclosure and
prompt correction of violations. This policy can not be applied to an enforcement action that
has already been initiated. Contact EPA’s Compliance Assistance and Sector Programs Division
(202‑564-2310) for information on the Small Business Policy or review the policy online at
http://www.epa.gov/compliance/incentives/smallbusiness/.

Small Business Administration National Ombudsman
The Small Business and Agriculture Regulatory Enforcement Ombudsman and ten Regional
Fairness Boards were established to receive comments from small businesses about federal
agency enforcement actions. The Ombudsman will annually rate each agency’s responsiveness
to small businesses. If you believe that you fall within the Small Business Administration’s
definition of a small business (based on your SIC designation, number of employees or

Appendix B: Example Letters to Owners/Operators After a Site Visit

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NPDES Permit Writers’ Manual for CAFOs

annual receipts, defined at 13 CFR 121.201) and wish to comment on federal enforcement and
compliance activities, contact the SBA’s Office of the National Ombudsman at 1-888-734-3247
or ombudsman@sba.gov. Please note that participation in this program does not relieve
you of your obligation to respond to an EPA request, administrative or civil complaint or
other enforcement action in a timely manner nor create any new rights or defenses under
law. In order to preserve your legal rights, you must comply with all rules governing the
administrative enforcement process. The ombudsman and fairness boards do not participate
in the resolution of EPA’s enforcement action.

Appendix B: Example Letters to Owners/Operators After a Site Visit

NPDES Permit Writers’ Manual for CAFOs

Appendix
Example NPDES CAFO
Permit Annual Report
Form

C

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C-1

Appendix C: Example NPDES CAFO Permit Annual Report Form

C-2

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C-3

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C-4

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NPDES Permit Writers’ Manual for CAFOs

Appendix

D

Example
Nutrient Management Plan
Recordkeeping Forms
CAFO Weekly Storage and Containment Structure Inspections Log Sheet . . . . . . . . . D-1
CAFO Weekly Storm Water Diversion and Channel Inspections Log Sheet. . . . . . . . . D-7
CAFO Nutrient Land Application Log Sheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D-13
Water Line Inspection Log Sheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D-15
Manure, Litter, and Process Wastewater Transfer Record From. . . . . . . . . . . . . . . . . . D-16

NPDES Permit Writers’ Manual for CAFOs

NPDES Permit Writers’ Manual for CAFOs

D-1

Appendix D: Example Nutrient Management Plan Recordkeeping Forms

D-2

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D-3

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D-4

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D-5

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D-6

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D-7

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D-8

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D-9

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D-10

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D-11

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D-12

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D-13

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D-14

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D-15

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D-16

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NPDES Permit Writers’ Manual for CAFOs

Appendix
Minimum Depth of Rain
at Which Runoff Begins

E

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Minimum Depth of Rain at Which Runoff Begins
This appendix provides a methodology for estimating the minimum depth of precipitation
required to produce runoff for a given field with a given runoff curve number.
Step 1: Estimate the runoff curve for the field or land area of concern. Table 3 in Appendix R
provides curve numbers for various combinations of land uses (e.g., row crops), cover treatment
or practices (e.g., contoured), and hydrologic conditions (e.g., poor). The runoff curve numbers
in this table represent Antecedent Runoff Condition III (e.g., saturated soils). To identify
corresponding runoff curve numbers for Antecedent Runoff Condition II (i.e., average conditions)
use either Appendix R-3 or Tables 2-2b and 2-2c in Urban Hydrology for Small Watersheds, USDANRCS, 1986 (see Appendix E-2).
To predict the possibility of runoff where rainfall is forecast in a season other than winter, it may
be reasonable to use runoff curves for Antecedent Runoff Condition II.
Step 2: Using Table 10-1 on page 10-7 of the USDA-NRCS National Engineering Handbook Part
630, Hydrology (see Appendix E-1); select the curve number (CN) for the field being investigated.
Step 3: For the selected curve number in Table 10-1, identify the minimum depth of precipitation
in inches required to produce runoff for a given runoff curve number (Column 5, designated with
the column header of Curve* starts where P =).

Appendix E: Minimum Depth of Rain at Which Runoff Begins

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NPDES Permit Writers’ Manual for CAFOs

Appendix E-1

National Engineering Handbook Table 10-1
Curve Numbers (CN) and Constants for the Case Ia = 0.2 S

Appendix E: Minimum Depth of Rain at Which Runoff Begins

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NPDES Permit Writers’ Manual for CAFOs

Appendix E-2

USDA Urban Hydrology for Small Watersheds (TR-55)

Appendix E: Minimum Depth of Rain at Which Runoff Begins

E-4

Appendix E: Minimum Depth of Rain at Which Runoff Begins

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Appendix E-3

Instructions for
Determining Precipitation Forecasts for CAFO Permits
Using the National Weather Service Website
WARNING: Do not be intimidated. This is much easier then it may seem at first. Once you learn
how to do this and save the results in your Favorites you can check both forecasts in less then a
minute (or up to a few minutes depending on your internet connection speed). In fact, you may
find these forecast models useful in planning other areas of work on your farm.
Start at this website: www.weather.gov/mdl/synop/products.php. Once you are there you may wish
to save it in your Favorites. If the website has changed or the required forecast models are not
longer available, please contact the Michigan Department of Environmental Quality Office listed
on your Certificate of coverage or on the cover page of your permit
1. Click on “Forecast Graphics” in the “GFS MOS (MAV)” box (near the center of the page).
2. In the column on the left side, in the drop down box under “Precipitation”, click on
“24H Prob.>= 0.50 in.”. Note: if it has been determined that a smaller precipitation
event is capable of producing runoff or erosion then use a smaller precipitation
probability such as “24H Prob. >=0.25 in.”.
3. This will bring up a map of the U.S. showing precipitation probabilities as colored
bands or areas for the upcoming 24 hour period. Precision is not ideal because it covers
all of the U.S. but estimate the color for the proposed land application area. If the
precipitation probability is 70% or greater (blue shades) then you should not land apply.
You can save the map in your favorites.
4. Underneath the map are day & time boxes such as “Tuesday” and “00” and “12”. That
would be Tuesday midnight and noon, GMT (Greenwich Mean Time) which is 5 hours
ahead of EST (Eastern Standard Time) and 4 hours ahead of EDT (Eastern Daylight
Time). So “Tuesday 00” would be 7 p.m. EST or 8 p.m. EDT Monday. The map forecast
is for the 24 hour period ending at the highlighted time. The first box, which will be
highlighted when you bring up the map, will give the map for the upcoming 24 hour
period. You can click on subsequent time periods to see future forecasts. You should
always check the immediate upcoming 24 hour forecast just prior to a planned land
application event.
After you have finished checking the maps use your back button or go to your Favorites to return
to the above website.
1. Click on “Text Message By Station List” in the “GFS MOS (MEX)” box (toward the right
side on the page).
2. In the list of states on the left side click on “Michigan”.

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3. In the list that comes up on the right side click in the box for the station closest to the
land application location. You may need to select 2 or 3 stations if none are close to
the land application area. If selecting more then one station, note the 4-letter station
designation after each station name so you know which chart is for which station.
4. Once you have selected the station(s) scroll to the bottom of the Michigan station list
and click on “Go to the bottom to submit now”. Then click on the “Submit Query” box.
5. You will now have a very confusing chart for each selected station (you can save this
page in your Favorites). Look down the left hand column for “Q24” and read across
the first number. It will be one digit from 0 to 6. This is the only number you need to be
concerned with. This number is the quantity precipitation forecast for the upcoming
24 to 48 hour period. 0 = no precipitation, 1 = 0.01" to 0.09", 2 = 0.1" to 0.24", 3 = 0.25" to
0.49", 4 = 0.5" to 0.99", 5 = 1.0" to 1.99" and 6 = > 2.0". If it is 4 or greater you may not land
apply. Note: if it has been determined that a smaller precipitation event is capable of
producing runoff or erosion then use a smaller precipitation quantity forecast number.
For example, if 0.35” of precipitation in 24 hours on a particular field will produce
runoff or erosion then you may not land apply if the number is 3 or greater.
6. You may need to check the charts 2 or 3 times in advance of a planned land application
event to determine the precipitation amount forecasted for the land application time
frame.
In the event that you are immensely curious as to what all the rest of the data on these charts
mean, then go back to the website at the top on these instructions and in the left hand column
click on “GFS Description” to get to an explanation page.
Once you have saved the map and charts in your Favorites, you can click on those links and get to
the current map or chart(s) with just one click!

Appendix E: Minimum Depth of Rain at Which Runoff Begins

NPDES Permit Writers’ Manual for CAFOs

Appendix
Voluntary Alternative
Performance Standards
for CAFOs

F

ii

Appendix F: Voluntary Alternative Performance Standards for CAFOs

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Introduction
The examples in this appendix are for informative purposes only. The examples assume, but do not
guarantee, that the confined animal feeding operation (CAFO) meets all applicable federal, state,
and local requirements.
The U.S. Environmental Protection Agency’s (EPA’s) long-term vision for CAFOs includes continuing
research and progress toward environmental improvement. CAFOs, U.S. Department of Agriculture
(USDA), land grant universities, state agencies, equipment vendors, and other agricultural
organizations are now working to develop new technologies to reduce nutrient, pathogen, and
other pollutant losses to surface water; ammonia and other air emissions; and groundwater
contamination from animal manure. In the future, as those technologies are developed and
improved, EPA believes that they could offer CAFOs the potential to match or surpass the pollutant
reduction achieved by complying with the current requirements. EPA believes that some CAFOs
will voluntarily develop and install new technologies and management practices equal to or
better than the current requirements described in the CAFO rule of this manual in exchange
for being allowed to discharge the treated effluent. (For the purposes of this appendix, the current
technology controls required under the CAFO effluent limitation guidelines (ELG) described in the
CAFO rule will be referred to hereafter as the baseline technology requirements.) That is why EPA
has created the voluntary performance standards program for CAFOs.
This appendix presents an overview of the baseline requirements and the voluntary performance
standards program, which includes a description of who can participate in the program, how
participation in the program will affect existing CAFO National Pollutant Discharge Elimination
System (NPDES) permits, and a step-by-step description of the requirements associated with
program participation.

A. Overview of the Baseline Requirements
As described in the CAFO rule, the baseline production area requirements for all existing beef,
dairy, heifer, veal, swine, and poultry CAFOs are the same. However, baseline requirements vary
for new operations. A summary of the requirements is presented in Table F-1.
Table F-1. Summary description of baseline requirements
Existing and new large beef, dairy, heifer and existing large swine, poultry and veal CAFOs
1. Baseline requirements prohibit the discharge of manure and process wastewaters.
2. A CAFO may discharge when rainfall events cause an overflow from a storage structure designed,
constructed, operated, and maintained to contain the following:
• All manure, litter, and all process wastewaters including manure, wastewater, and other wastes
accumulated during the storage period as reflected by the design storage volume
• Direct precipitation from a 25-year, 24-hour rainfall event
• Associated runoff from a 25-year, 24-hour rainfall event

Appendix F: Voluntary Alternative Performance Standards for CAFOs
A. Overview of Baseline Requirements

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NPDES Permit Writers’ Manual for CAFOs

B. Overview of the Voluntary Performance
Standards Program
Under the voluntary performance standards program, existing and new Large beef, heifer,
and dairy CAFOs and existing Large swine, poultry, and veal CAFOs are allowed to discharge
process wastewater that have been treated by technologies that the CAFO demonstrates results
in equivalent or better pollutant removals from the
production area than would otherwise be achieved by
Program Benefits
the baseline requirements.

B.1. Program Participation
All CAFOs electing to participate in the program should
have a good compliance history (e.g., no ongoing
violations of existing permit standards or history of
significant noncompliance). In most cases, participation
will result in an individual NPDES permit addressing
the site-specific nature of the alternative technology and
establishing site-specific discharge limitations.

CAFOs are expected to derive
substantial benefits from participating
in this program through greater
flexibility in operation, increased
goodwill of neighbors, reduced odor
emissions, potentially lower costs,
and overall improved environmental
stewardship. EPA is considering other
possible incentives to encourage
participation in this program.

B.2. Pollutants of Concern
In general, all CAFOs applying for the voluntary performance standards program must design the
treatment technology to achieve equal or less quantities of 5-day biochemical oxygen demand
(BOD5), total nitrogen (N) (ammonia, nitrite/nitrate, and organic N), total phosphorus (P), and
total suspended solids (TSS) than the baseline system. EPA selected those parameters because
of their high concentrations in manure-type wastestreams and their impact on surface water
quality if not treated. In addition, many conventional wastewater treatment technologies, in the
process of treating those four selected pollutants, will result in treatment and removal of other
pollutants. To qualify for voluntary alternative performance standards, the CAFO may also be
required to remove other specific pollutants, such as pathogens and metals, if such pollutants
are present in the wastestream at concentrations that could affect surface water quality, as
determined appropriate by the permitting authority.

B.3. Required Technical Analysis
CAFOs requesting site-specific effluent limitations to be included in NPDES permits must submit
a supporting technical analysis and any other relevant information and data that would support
such site-specific effluent limitations. For more information, see Section C of this appendix.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
B. Overview of the Voluntary Performance Standards Program

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B.4. Validation of Equivalent Pollutant Reductions
The CAFO must attain the limitations and requirements of a permit on the basis of alternative
technologies as of the date of permit coverage (Title 40 of the Code of Federal Regulations [CFR]
section 412.31(a)(3). If those alternative limits will not be met as of the date of permit coverage,
such as because of startup of certain wastewater
treatment technologies, the permitting authority
General versus Individual NPDES Permits
would need to incorporate a compliance schedule into
A general NPDES permit is written to cover a
an enforceable order that would establish milestones
category of point sources with similar characteristics
for implementing the alternative technologies and
for a defined geographic area. The majority of
fully meeting the permit limitations. The permitting
CAFOs may appropriately be covered under NPDES
authority should consider whether it is appropriate to
general permits because CAFOs generally involve
select a permit term that is less than 5 years to allow
similar types of operations, require the same kinds
the permitting authority to evaluate whether the
of effluent limitations and permit conditions, and
alternative technologies have resulted in the permit
discharge the same types of pollutants.
limitations being met.
Individual NPDES permits might be most appro-

If the permitting authority grants a request for voluntary
priate for CAFOs that are exceptionally large
alternative performance standards, the CAFO should,
operations, are undergoing significant expansion,
have historical compliance problems, or have signifiat a minimum, be required to take monthly effluent
cant environmental concerns. Individual permits will
samples from the treatment system to verify continued
generally include all the permit conditions contained
permit compliance. The permitting authority may
in the general NPDES permit and some additional
determine that the CAFO must take more frequent
requirements specific to the permitted facility. Addisamples (such as during startup) or collect samples
tional requirements could include liners and covers
on a basis other than monthly (such as during all
for manure and wastewater storage units and more
discharge events in the case of intermittent discharging
frequent water quality monitoring.
technologies). CAFOs should be required to analyze
for the following pollutants: BOD5, total N, total P, and
TSS. The permitting authority may also require a CAFO to monitor other pollutants regularly. If
monthly pollutant discharges from the alternative treatment system are greater than specified in
the NPDES permit, a CAFO could be subject to both state and EPA enforcement actions.

B.5. Relationship to Existing NPDES Permits
EPA expects that most CAFOs will be subject to a general, rather than an individual, permit
that requires compliance with the baseline effluent guidelines requirements. If a CAFO decides
to pursue voluntary performance standards based on a treatment technology that allows
a discharge, EPA expects the permit authority to require the CAFO prepare and submit an
application for an individual NPDES permit. The application will include general information
about the CAFO (e.g., ownership, responsible persons, location, receiving stream), waste
characteristics, information about the treatment system including design and operational
parameters, and expected effluent quality from the proposed treatment system. A CAFO may
not discharge from the alternative treatment system until the permitting authority has issued an
NPDES permit that allows the discharge.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
B. Overview of the Voluntary Performance Standards Program

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NPDES Permit Writers’ Manual for CAFOs

C. Step-By-Step Requirements for Participation in the
Voluntary Performance Standards Program
The voluntary performance standards program has two main requirements: the CAFO must
estimate the pollutant discharge associated with the baseline system and must demonstrate that
the alternative treatment technology achieves an equivalent or better reduction in the quantity of
pollutants discharged from the production area. This section provides detailed recommendations
for how such showings should be made, along with a description of the information that must be
submitted to the permitting authority to obtain alternative performance standards.

C.1. Determining Baseline Pollutant
If a CAFO decides to participate in the voluntary performance standards program, the CAFO must
conduct a technical analysis to estimate the pollutant discharge associated with the baseline1
waste management system (e.g., anaerobic treatment lagoon). At a minimum, the technical
analysis must include the information in the text box at
right [see 40 CFR part 412.31(a)(2)].
Technical Analysis of Discharge
40 CFR part 412.31(a)(2) …The technical
analysis of the discharge of pollutants must
include
(A) All daily inputs to the storage system,
including manure, litter, all process waste
waters, direct precipitation, and runoff.
(B) All daily outputs from the storage system,
including losses due to evaporation, sludge
removal, and the removal of wastewater for use
on cropland at the CAFO or transport off site.
(C) A calculation determining the predicted
median annual overflow volume based on a
25-year period of actual rainfall data applicable
to the site.
(D) Site-specific pollutant data, including N, P,
BOD5, TSS, for the CAFO from representative
sampling and analysis of all sources of input
to the storage system, or other appropriate
pollutant data. (E) Predicted annual average
discharge of pollutants, expressed where
appropriate as a mass discharge on a daily
basis (lbs/day), and calculated considering
paragraphs (a)(2)(i)(A) through (a)(2)(i)(D) of
this section.

In a limited number of circumstances, the calculated
median annual overflow volume based on a 25-year
period of actual rainfall data may be zero. In those
instances, the permit authority may allow the CAFO to
calculate an average overflow volume for the 25-year
period.
One approach for estimating pollutant discharges is to
use a computer simulation model, spreadsheet, or similar
program. One can either develop a new model or revise
an existing model that estimates pollutant discharges
from waste management systems. The models can be
used to evaluate site-specific climate and wastewater
characterization data to project the pollutant discharge
from a baseline system. The model should evaluate the
daily inputs to the waste management system, including
all manure, litter, all process wastewaters, direct
precipitation, and runoff. The model should also evaluate
the daily outputs from the waste management system,
including losses due to evaporation, sludge removal,
and the removal of wastewater for use on cropland at the
CAFO or transported off-site. CAFOs can use the model
to predict the median annual overflow from the storage
system that would occur over a 25-year period. Next, the
CAFO should use the overflow predictions, combined

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

NPDES Permit Writers’ Manual for CAFOs

F-5

with representative pollutant concentrations in the overflow, to predict the annual average
discharge of pollutants (including nitrogen, phosphorus, BOD5, and TSS) over the 25 years
evaluated by the model. For the complete list, see 40 CFR part 412.31(a)(2)(i)(E).
Site-specific information that a CAFO should gather and input to the model to calculate the
predicted annual discharge of pollutants from the baseline system includes the following [also
see 40 CFR part 412.31(a)(2)]:
▶ Data on actual local precipitation from the past 25 years. Precipitation data are available
from the National Weather Service and possibly a local airport. One can also obtain
local precipitation data from EPA’s Better Assessment Science Integrating point and
Nonpoint Sources (BASINS) model at http://www.epa.gov/OST/BASINS/b3webwn.htm.
State weather data are at http://www.epa.gov/ost/ftp/basins/wdm_data/. Historical
weather can also be obtained from National Climatic Data Center.
▶ Soil type and permeability in drylot areas. Site-specific soil permeability data can be
obtained from the local Soil Conservation District office.
▶ The rate of evaporation from the storage system (e.g., lagoon, pond, holding tank).
Evaporation rate data are available from the National Weather Service or EPA’s BASINS
model website.
▶ The concentration of BOD5, total N, total P, TSS, and other pollutants as required by the
Director, measured in a representative sample collected from the waste management
system.
▶ Starting volume in the waste management system based on process wastes and runoff
collected since the last land application or waste management system pump-out or
sludge cleanout or both.
▶ Projected total design storage volume to store manure, wastewater, and other wastes
accumulated during the storage period as reflected by the design storage volume (see
Chapter 5.3 of this document).
▶ Change in the waste management system’s volume due to the estimated daily flow of
process wastes.
▶ Change in the storage system volume due to direct precipitation and evaporation.
▶ Change in the storage system volume due to runoff from open lot areas.
▶ Change in volume due to waste management system pump-out or sludge cleanout and
land application.
The model should calculate the net change in the volume of the liquid storage area daily and add
it to the previous day’s total. If the total volume is greater than the maximum design volume,
the excess volume overflows. Also, CAFOs can calculate the mass pollutant discharge from the

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

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NPDES Permit Writers’ Manual for CAFOs

overflow by multiplying the overflow by the pollutant concentration (BOD5, total N, total P, TSS)
measured in the representative sample.
Examples 1 and 2 at the end of this appendix present the results of a technical analysis conducted
for example dairy and swine CAFOs, respectively.

C.2. Demonstrating That an Alternative Control Technology
Achieves Equivalent or Better Pollutant Reductions
EPA recommends that CAFOs follow the steps shown below to demonstrate that an alternative
control technology will achieve equivalent or better pollutant reductions:
▶ Measuring volume or quantity of manure, wastewater, and runoff generation from
production areas.
▶ Collecting samples of manure, wastewater, and runoff to determine raw or untreated
pollutant concentrations for treatment system design using the same pollutant
parameters as measured for a baseline.
▶ Preparing a conceptual design of the treatment system showing equipment sizing,
operational requirements, and expected pollutant reductions by each treatment step.
▶ Estimating the volume and frequency of discharge from the treatment system.
▶ Estimating or measuring the concentration of the effluent from the treatment system.
▶ Results of pilot testing to verify the treatment system will achieve equivalent or better
pollutant reductions than baseline for all required constituents (including BOD5, total
N, total P, and TSS) and to gather information for design of the full-scale treatment
system. Any pilot testing needs to be related to representative/typical production and
climate conditions expected at the CAFO. Therefore, multiple testing episodes or sites
might be necessary to adequately capture the actual conditions at the CAFO. Consider
on-site pilot testing to demonstrate that the proposed system will work at the CAFO.
Examples 1 and 2 summarize the methods that could be used by the example CAFOs to
determine if an alternative treatment system performed equivalent to or better than the baseline
system. In the examples, the permit authority would require the CAFO to continue to collect
testing data until the alternative technology has been proven at the site. Thereafter, the CAFO
might need to collect samples only frequently enough to demonstrate compliance with their
NPDES permit limitations.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

NPDES Permit Writers’ Manual for CAFOs

F-7

Can a CAFO Demonstrate Equivalency Using Practices Already in
Existence at the Site?
Yes. If the practices already in place at the operation provide equivalent or better
pollutant reductions than the predicted average annual pollutant discharge for the
baseline requirements, the CAFO can apply for an alternative performance standard.
Example 3 shows how data from an existing pollution prevention/treatment system
were compared to the baseline system to develop site-specific permit limits for an egg
production facility.

C.3. Obtaining an Alternative Performance Standard
The next step in participating in the voluntary performance standards program is to submit an
application to the permitting authority along with the technical analyses, conceptual design,
results of any pilot-scale testing and any other relevant data before constructing the full-scale
treatment system. The permitting authority should review the application, technical analyses,
and conceptual design, and then compare the pilot-scale testing results with the predicted
annual average discharge of pollutants to verify that the proposed treatment system is reasonable,
appropriate, and will likely achieve the predicted results. In addition, the permit authority should
confirm that the quantity of pollutants discharged from the production area is equal to or less
than the quantity of pollutants discharged under baseline. The Director has the discretion to
request additional information to supplement the CAFO’s application, including conducting an
on-site inspection of the CAFO. 40 CFR § 412.31(a)(2)(E)(ii). Once an application is approved, a
CAFO can proceed with detailed design and construction of the alternative control technology.
After the treatment system’s construction but before start-up [see 40 CFR part 412.31(a)(3)], the
CAFO must obtain an NPDES permit specifying the discharge limitations. Also see Section B.4 of
this appendix.

Footnotes
1

Recall a baseline system at the CAFO is a system that meets the requirements as described in the CAFO Rule [see
40 CFR part 412.31(a)(1)].

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

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NPDES Permit Writers’ Manual for CAFOs

Example 1. Whole Milk Dairy, Lancaster, Pennsylvania
Background
Whole Milk Dairy (WMD) is a Large CAFO in Lancaster County, Pennsylvania. WMD milks 1,200 dairy cows
per day, plus manages 400 heifers and 400 calves. Milk cows are confined in a 550,000-square-foot-area
containing three free stall barns, the milking parlor, and yard. Free stall barn alleys are cleaned three times
a day (every 8 hours) using a flush system. Sawdust is used for bedding in the free stall barn. Silage is kept
covered. All flush water, cow wash-water, and parlor cleanup and sanitation water is directed to the existing
3,351,252-cubic-foot manure holding lagoon.
All liquids in the holding lagoon are applied to crop land four times each year consistent with the site’s NMP.
Thus, the lagoon has 90 days of storage capacity. To help show the storage structure has adequate capacity,
WMD assumes that the storage volume is never less than the accumulated sludge volume plus the minimum
treatment volume. Although solids are periodically removed and thus more volume is available to store
process wastewater, runoff, and precipitation, this conservative assumption reserves the sludge volume for
the maximum amount of accumulated solids over the storage period.
Approximately 40 percent of the milk cow confinement area is paved or roofed. Precipitation from roofed
areas drains onto the paved portion of the milk cow confinement area before being discharged to the
manure holding lagoon. All paved areas have curbing to contain manure and precipitation. Unpaved areas
have reception pits to collect manure and precipitation before discharge to the manure holding lagoon.
Heifers and calves are managed on a non-paved 300,000-square-foot-dry lot that discharges to the manure
holding lagoon. Any overflows from the lagoon might eventually reach a receiving surface waterbody (in this
case, the Susquehanna River).

Summary of baseline overflow volume and pollutant loading calculations
Process Wastewater Generation:

25,857 ft 3/day (193,400 gal/day)

Sludge Volume (constant):

870,807 ft 3

Minimum Treatment Volume (constant):

1,530,000 ft 3

Total Existing Storage Lagoon Volume:

3,351,252 ft 3 (25 million gallons)

Volume in Lagoon at Start:

2,400,807 ft 3 (Sludge Volume + Minimum Treatment Volume)

Precipitation Volume (median):

40 in/yr

Evaporation Rate (median):

57 in/yr

Runoff (median):

17,033 ft 3/yr

Liquid/Solids Removal for Crop Application: Completely dewater all lagoon liquids four times per year

Calculated baseline overflow volume method
Daily Accumulation of Lagoon Liquids (ft3/day) = Process Waste (ft3/day) + Runoff (ft3/day) + ((PrecipitationEvaporation (ft/day)) x Lagoon Surface Area (ft 2)
Volume of Lagoon Liquids (ft3) = Previous Days’ Volume (ft3) + Daily Accumulation of
Lagoon Liquids Volume (ft3/day)

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

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NPDES Permit Writers’ Manual for CAFOs

Example 1. Whole Milk Dairy, Lancaster, Pennsylvania (continued)
If the Volume of Lagoon Liquids (ft 3) is greater than the following:
Existing Storage Lagoon Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment Volume (ft3)], then
Overflow Volume = Volume of Lagoon Liquids (ft 3) - [Existing Storage Lagoon
Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment
Volume (ft 3)]; and
Volume of Lagoon Liquids (ft 3) is adjusted to the following:
[Existing Storage Lagoon Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment Volume (ft 3)] (the
maximum volume of liquids the lagoon can store)
If it is a land application day:
The Volume of Lagoon Liquids (ft 3) = 0
Calculated Overflow Volume for WMD: 57,386 ft 3/yr (429,247 gal/yr)
WMD collected a representative sample of liquid from the storage lagoon to calculate the annual pollutant
discharge of BOD5, total N, total P, and TSS as a result of the overflow volume. The sample was collected
from the top 12 inches of the lagoon surface because the majority of overflow will likely be attributed to that
zone. The sampling results are shown below:
BOD5:

600 mg/L

(5.0 lbs per 1,000 gallons)

Total N:

268 mg/L

(2.2 lbs per 1,000 gallons)

Total P:

208 mg/L

(1.7 lbs per 1,000 gallons)

TSS:

1,500 mg/L

(12.5 lbs per 1,000 gallons)

On the basis of the overflow and the measured concentration, the annual pollutant discharges from the
lagoon were calculated by multiplying the flow by the concentration as shown in the example for BOD5
below:
BOD5: 600 mg/L x 3.785 L/gal x 429,247 gal/yr x 2.2 lbs/kg x 1 kg/10 6 mg = 2,145 lbs/yr
A summary of the pollutant loadings based on the overflow rate and concentration is shown below.
BOD5:

2,145 lbs/yr

Total N:

958 lbs/yr

Total P:

743 lbs/yr

TSS:

5,362 lbs/yr

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

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Example 1. Whole Milk Dairy, Lancaster, Pennsylvania (continued)

Diagram of baseline waste management system
The following figure is a block diagram of WMD summarizing the inputs and outputs from the manure
storage lagoon and the overflows and pollutant loadings. Any overflows from the lagoon eventually reach a
surface waterbody (in this case, the Susquehanna River).
Soil Infiltration

Parlor
with
Flush

Evaporation:
57 in/yr

Precipitation

3 Free Stall Barns with Flush
Alleys and Yard

Process Waste: 70,591,000 gal/yr

Total Cows: 1,200
Barn and Yard Area: 550,000 ft 2
Covered or paved portion: 40%

Runoff: 127,400 gal/yr

Soil Infiltration

Precipitation:
40 in/yr

Existing Manure
Collection Lagoon
Volume: 3,351,252 ft3

Precipitation

To Land
Application
Overflow to
Susquehanna River:
429,247 gal/yr

Calf and Heifer Dry Lot
Total Calves: 400
Total Heifers: 400
Drylot Area: 300,000 ft 2
Paved Portion: 0%

BOD5: 2,145 lbs/yr
Total Nitrogen: 958 lbs/yr
Total Phosphorus: 743 lbs/yr
Total Suspended Solids: 5,362 lbs/yr

Waste characterization and alternative treatment system evaluation
WMD in cooperation with its consultant, Tick Engineering, has decided to voluntarily pursue an alternative
to its existing lagoon to have a constant discharge of treated water to the Susquehanna River. The treatment
train it selected consists of primary clarification, aerobic biological treatment, and final polishing using an
engineered wetland. Tick Engineering conducted pilot-scale testing of the system June 15 to November 15 at
WMD using actual process wastewater. The conceptual design calculations and pilot-scale treatment test are
summarized below.

Waste flow and characterization
Tick Engineering conducted a daily composite sample of manure, flush water, wash water, parlor cleanup and
sanitation water and rainwater during a 7-day operational period in April 2003 to characterize the wasteload
discharged to the storage lagoon. The combined volume of manure, flush water, wash water, parlor cleanup
water and rainwater was also measured during the 7-day sampling period in April, 2003. The average daily
flow to the lagoon, which included one day of rainfall was 176,410 gallons. Waste characterization data and
calculated average daily loading to the treatment system are summarized below:

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

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NPDES Permit Writers’ Manual for CAFOs

Example 1. Whole Milk Dairy, Lancaster, Pennsylvania (continued)

Pollutant
BOD5:

Concentration
(mg/L)

Influent
(lbs/day)

1,701

2,496

Total N:

478

702

Total P:

74

109

12,269

18,018

TSS:

Daily pollutant loadings were calculated by multiplying the concentration for each constituent by the average
daily flow as shown in the example below for BOD5:
BOD5 Loading: 1,701 mg/L x 3.785 L/gal x 1 kg/1,000,000 mg x 2.2 lbs/kg x 176,410 gal/day = 2,496 lbs/day
The treatment system design is based on a flow excess of 20% or 211,690 gallons per day. Flows greater
than 211,690 gal/day will overflow back to the existing 3,351,252-cubic-foot lagoon. During dry-weather
periods, excess water and direct precipitation from the lagoon will be pumped back to the beginning of the
treatment system for processing. The following figure is a flow diagram showing the treatment equipment
and sizes, flows in and out of each treatment unit, and the pollutant reductions by each treatment step. Note
that WMD will have the capability of recycling nearly 90,000 gallons per day of treated effluent for manure
flushing.

Alternative treatment system effectiveness
The average concentration of target pollutants measured in the effluent from the pilot-scale treatment
system during the 6-month study is shown below. The calculated monthly loadings for the full-scale
treatment system is based on an average daily flow of 176,410 gallons entering the treatment system minus a
recycle flow of 90,000 gallons per day for manure flushing.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

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NPDES Permit Writers’ Manual for CAFOs

Example 1. Whole Milk Dairy, Lancaster, Pennsylvania (continued)

Diagram of alternative treatment system

Parlor
with
Flush

Flow: 211,680 gal/day
BOD: 2,600 lbs/day
TSS: 18,700 lbs/day
Nitrogen: 730 lbs/day
Phosphorus: 113 lbs/day

3 Free Stall Barns with Flush
Alleys and Yard
Total Cows: 1,200
Barn and Yard Area: 550,000 ft 2
Covered or paved portion: 40%

Flow: 198,860 gal/day
BOD: 1,248 lbs/day
TSS: 3,604 lbs/day
Nitrogen: 350 lbs/day
Phosphorus: 55 lbs/day

Runoff

Calf and Heifer Dry Lot

Excess Precipitation

Primary
Overflow
Clarifier
Area: 310 ft 2
Length: 36' Sludge:
Width: 9' 12,800 gal/day
Depth: 8'

Waste
Biosolids:
5,070 gal/day

Alum

Total Calves: 400
Total Heifers: 400
Drylot Area: 300,000 ft 2
Paved Portion: 0%

34' dia.

15 ft

Flush Water
Collection Sump
Flush Water Recycle:
90,000 gal/day
Flow: 106,650 gal/day
BOD: 5 lbs/day
TSS: 8 lbs/day
Nitrogen: 0.3 lbs/day
Phosphorus: 2 lbs/day

Aerobic/
Anoxic
Sequencing
Batch Reactor
Volume:
99,700 gal

34' dia.

To Land
Application

Aerobic/
Anoxic
Sequencing
Batch Reactor
Volume:
99,700 gal
Flow: 196,650 gal/day
BOD: 33 lbs/day
TSS: 49 lbs/day
Nitrogen: 2 lbs/day
Phosphorus: 7 lbs/day

Engineered Wetland
Area: 0.6 acres, Depth: 3 feet
Engineered Wetland
Area: 0.6 acres, Depth: 3 feet

Whole Milk Dairy
Lancaster, PA

Engineered Wetland
Area: 0.6 acres, Depth: 3 feet

NPDES Discharge

Existing
Manure
Collection
Lagoon
(covered)
Volume:
3,351,252 ft 3

Comparison of the baseline overflow to the discharge from the alternative
treatment system
Pollutant
BOD5:

Baseline overflow (lbs/yr)

Treatment system discharge (lbs/day)

2,145

1,830

Total N:

958

110

Total P:

743

730

5,362

2,920

TSS:

Conclusion: The loadings comparison clearly shows the proposed treatment system consisting of primary
clarification, aerobic biological treatment and final polishing using an engineered wetland would achieve
a quantity of pollutants discharged from the production area that is equal to or less than the quantity of
pollutants that would be discharged using baseline treatment. Note: This analysis pertains to the technologybased requirements of the CAFO rules and does not include an assessment of whether a discharge would
meet the state’s water quality standards.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

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NPDES Permit Writers’ Manual for CAFOs

Example 2. KF Pork Producers, Davenport, Iowa
Background
KF Pork Producers (KFP) is a Large CAFO in Scott County, Iowa. KFP has 7,000 grower swine with an average
weight of approximately 140 pounds. Swine are housed in a 57,400-square-foot-barn with 10 confinement
pens. Manure is washed from pens daily using a flush system. All manure and flush water drains into storage
tanks beneath the partially slotted concrete floor. Storage tanks are emptied daily by pumping the manure
and flush water to an existing 3,931,800-cubic-foot manure holding lagoon.
KFP, in consultation with local residents, avoids de-watering the storage structure on weekends and holidays.
Liquids in the holding lagoon are applied to crop land (to the maximum daily hydraulic loading) on the 7th,
14th, 21st, and 28th days of each month during the freeze-free period between April 21 and September 14,
assuming that there has been no significant precipitation during the 3 days before the day of application.
(The nutrient applications are tracked by KFP’s NMP and are not further considered here.) KFP assumes
that the storage volume is never less than the accumulated sludge volume plus the minimum treatment
volume. Although there are times that solids are removed and more space is available for process wastewater,
runoff, and precipitation, that conservative assumption reserves storage space for the maximum amount of
accumulated solids over the storage period.

Summary of baseline overflow volume and pollutant loading calculations
Process waste generation:

8,356 ft 3/day (62,500 gal/day)

Sludge Volume (constant):

486,091 ft 3 (3.6 million gal)

Minimum Treatment Volume (constant):

661,500 ft 3 (4.9 million gal)

Total Existing Storage Lagoon Volume:

3,931,800 ft 3 (29.4 million gal)

Volume of Liquids and Solids in Lagoon at
Start:

1,206,083 ft 3 (Sludge Volume + Minimum Treatment Volume
+ Accumulated Process Wastes Since Last Liquid Application)

Precipitation Volume (average):

26 in/yr

Evaporation Rate (average):

98 in/yr

Liquid/Solids Removal for Crop Application: Land apply lagoon liquids to the maximum hydraulic loading
of the crop land on days 7, 14, 21, and 28 of each month
unless there has been precipitation in the past 3 days before
the application day (That occurs between the freeze-free days
between April 21 and September 14)

Calculated baseline overflow volume method
Daily Accumulation of Lagoon Liquids (ft3/day) = Process Waste (ft 3/day) + [Precipitation – Evaporation]
(ft/day) x Lagoon Surface Area (ft 2)
Volume of Lagoon Liquids (ft3) = Volume of Lagoon Liquids from Previous Day (ft 3) + Daily
Accumulation of Lagoon Liquids (ft 3)

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

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Example 2. KF Pork Producers, Davenport, Iowa (continued)
If the Volume of Lagoon Liquids (ft 3) is greater than the following:
Existing Storage Lagoon Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment Volume (ft3)], then
Overflow Volume = Volume of Lagoon Liquids (ft 3) - [Existing Storage Lagoon
Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment
Volume (ft 3)]; and
Volume of Lagoon Liquids (ft 3) is adjusted to the following:
[Existing Storage Lagoon Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment Volume (ft 3)]
(the maximum volume of liquids the lagoon can store)
If it is an application day (day 7, 14, 21, or 28 of the period between April 21 and September 14), the
Volume of Lagoon Liquids (ft 3) = Volume of Lagoon Liquids (ft 3) - Max Hydraulic Loading (ft3)
Calculated Overflow Volume for KFP: 158,419 ft 3/yr (1,184,970 gal/yr)
KFP collected a representative sample of liquid from the storage lagoon to calculate the annual pollutant
discharge of BOD5, total N, total P, and TSS as a result of the overflow volume. The sample was collected
from the top 12 inches of the lagoon surface because the majority of overflow will likely be attributed to that
zone. The sampling results are shown below:
BOD5:

1,650 mg/L

Total N:

270 mg/L

Total P:

102 mg/L

TSS:

3,000 mg/L

On the basis of the overflow and the measured concentration, the annual pollutant discharges from the
lagoon were calculated by multiplying the flow by the concentration as shown in the example for BOD5
below:
BOD5: 1,650 mg/L x 3.785 L/gal x 1,184,970 gal/yr x 2.2 lbs/kg x 1 kg/10 6 mg = 16,280 lbs/yr
A summary of the pollutant loadings based on the overflow rate and concentration is shown below.
BOD5:

16,280 lbs/yr

Total N:

2,660 lbs/yr

Total P:

1,010 lbs/yr

TSS:

29,600 lbs/yr

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

F-15

NPDES Permit Writers’ Manual for CAFOs

Example 2. KF Pork Producers, Davenport, Iowa (continued)

Diagram of baseline waste management system
The following figure is a block diagram of KFP summarizing the inputs and outputs from the manure storage
lagoon and the overflows and pollutant loadings. Any overflows from the lagoon discharge to a surface
waterbody (in this case, the Mississippi River).
Clean Flush Water

Air Emissions
Ammonia: 80 lbs/yr
H2S: 10 lbs/day

Swine barn with confinement
pens, partly slatted floor, deep
pit storage and liquid manure
handling

Direct Precipitation: Evaporation:
26 in/yr
98 in/yr

Flow: 62,500 gal/day

Volume: 3,931,800 ft 3
Depth: 25 ft

Number of pigs: 7,000
Barn area: 57,400 sq ft
Barn height: 12 ft
Barn air volume: 688,000 cu ft

Flow: 1,184,970 gal/yr
BOD: 16,280 lbs/yr
Nitrogen: 2,660 lbs/yr
TSS: 29,600 lbs/yr
Phosphorus: 1,010 lbs/yr

Existing Storage
Lagoon

Land Application
(4x/month)
Overflow to Mississippi River

KF Pork Producers
Current Manure
Handling Practices

Waste characterization and treatment system evaluation
KFP realized it was not cost-effective to haul excess nutrients in the liquid manure. KFP, in cooperation with
its consultant, WB Engineering, conducted a whole-farm audit to determine if pollutant releases could be
reduced at the facility by applying new technologies. WB Engineering examined discharges of pollutants
from lagoon overflows, estimated air emissions of ammonia and hydrogen sulfide, and worked with KFP to
determine if changes in swine feed rations could lower the amount of ammonia and P entering the manure.
Finally, WB examined manure application rates to determine if more frequent removals of manure/sludge
from the lagoon could provide additional storage capacity and less frequent overflows.
As a result of the whole-farm audit, KFP decided to further evaluate a new wastewater treatment system
plus an off-gas treatment system for air removed from both the swine barn and manure pits. Changes in
feed rations were not implemented on recommendations from both an animal nutritionist and the local
agricultural extension agent, and additional application rates of manure to KFP’s crop land would have
exceeded nutrient requirements according to the facility’s NMP.
The treatment train selected for KFP consists of primary clarification, a vibrating membrane filtration system,
and final polishing using a biological trickling filter. For off-gas from the swine barn and manure pits, a
biofilter using inorganic media was selected to remove ammonia and hydrogen sulfide. Pilot-scale testing
of both the wastewater and air treatment system was conducted March 20 to September 20, 2003, by WB
Engineering. Pilot 20 2003 by WB Engineering. A summary of the conceptual design calculations and pilotscale treatment test results are below.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

F-16

NPDES Permit Writers’ Manual for CAFOs

Example 2. KF Pork Producers, Davenport, Iowa (continued)

Waste flow and characterization
WB Engineering collected a daily composite sample of manure and flush water during a 7-day operational
period in March 2003 to characterize the wasteload discharged to the storage lagoon. The volume of manure
and flush water was also measured during the 7-day sampling period in April, 2003. The average daily flow
to the lagoon was 62,500 gallons. Waste characterization data and calculated average daily loading to the
treatment system for the target pollutants are summarized below:

Pollutant

Concentration
(mg/L)

BOD5:

Influent
(lbs/day)

3,766

1,960

Total N:

753

392

Total P:

301

157

11,863

6,174

TSS:

Daily pollutant loadings were calculated by multiplying the concentration for each constituent by the average
daily flow as shown in the example below for BOD5:
BOD5 Loading: 3,766 mg/L x 3.785 L/gal x 1 kg/1,000,000 mg x 2.2 lbs/kg x 62,500 gal/day = 1,960 lbs/day
The wastewater treatment system design is based on a flow excess of 20% or gallons per day. Flows greater
than 75,000 gallons per day will overflow to the existing 1,500,000-cubic-foot lagoon. During dry-weather
periods, excess water from the lagoon will be pumped back to the beginning of the treatment system for
processing. Note that KFP will have the capability of recycling nearly 22,600 gallons per day of treated
effluent for manure flushing.
Off-gas from the swine barn and deep pit areas was characterized by collecting air samples from areas near
the exit fans. The average concentration of ammonia and hydrogen sulfide measured in the off-gas was 54
ppm and 4 ppm, respectively. On the basis of a measured exhaust rate from all the exit fans for the barn and
pit areas, WB Engineering estimates approximately 80 lbs/day of ammonia and approximately 10 lbs/day of
hydrogen sulfide is emitted to the atmosphere. Design of the biofilter for treatment of off-gas was provided
by BIOREM and consists of new fans and duct work to move air through a single discharge point and an inground biofilter to destroy ammonia and hydrogen sulfide.

Treatment system effectiveness
The average concentration of target pollutants measured in the effluent from the pilot-scale wastewater
treatment system during the 6-month study is shown in the table below. The calculated monthly loading for
the full-scale treatment system is based on an average daily flow of 25,250 gallons. The remaining 37,750
gallons of water that enter the treatment system is used for either recycle or contains concentrated treatment
residuals that are discharged to the existing storage lagoon. KFP now has the additional flexibility to collect
solids and concentrated nutrients from the existing sludge lagoon and haul them off-site for other uses.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

F-17

NPDES Permit Writers’ Manual for CAFOs

Example 2. KF Pork Producers, Davenport, Iowa (continued)

Diagram of alternative treatment system
NH3: 25 lbs/day
H2S: 1.3 lbs/day

Flush Water

Biofilter

Land Application
(4x/month)
2,200 gal/day

Flow: 62,500 gal/day
BOD: 1,960 lbs/day
TSS: 6,170 lbs/day
Nitrogen: 390 lbs/day
Phosphorus: 160 lbs/day

NH3: 80 lbs/day
H2S: 8 lbs/day

Primary Clarifier
Surface area: 73 ft 2
Length: 17'
Width: 4.5'
Depth: 5'

Flush
collection
sump

Swine barn with farrowing
crates, partly slatted floor,
deep pit storage and liquid
manure handling

Flow: 60,300 gal/day
BOD: 980 lbs/day
TSS: 1,850 lbs/day
Nitrogen: 157 lbs/day
Phosphorus: 78 lbs/day

Number of pigs: 7,000
Barn area: 57,400 sq ft
Barn height: 12 ft
Barn air volume: 688,000 cu ft

Existing Storage
Lagoon
Volume: 3,931,800 ft 3
Depth: 25 ft

Effluent
collection
sump

Recycle Flow: 22,600 gal/day
Solids:
12,100 gal/day
Trickling Filter Flow: 25,600 gal/day
To the
Mississippi River
NPDES Discharge

Vibratory Shear
Enhanced Membrane

26' dia.

Secondary
Clarifier

Flow: 25,250 gal/day
59 ft 2
BOD: 3,285 lbs/yr
Settling Area
Nitrogen: 2,215 lbs/yr
TSS: 2,190 lbs/yr
Phosphorus: 1,460 lbs/yr

BOD: 196 lbs/day
TSS: 9 lbs/day
Nitrogen: 33 lbs/day
Phosphorus: 11 lbs/day

Biological
Trickling
Filter
8 ft
Recycle Ratio: 0.5
Sludge to Lagoon: 350 gal/day

KF Pork Producers
Davenport, IA

Comparison of the baseline overflow to the discharge from the alternative
treatment system
Pollutant
BOD5:

Baseline overflow (lbs/yr)

Treatment system discharge (lbs/day)

16,280

3,285

Total N:

2,664

2,215

Total P:

1,006

1,460

29,602

2,190

TSS:

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

F-18

NPDES Permit Writers’ Manual for CAFOs

Example 2. KF Pork Producers, Davenport, Iowa (continued)
The average concentration of ammonia and hydrogen sulfide measured in the off-gas from the biofilter
during the 6-month pilot-scale treatment test is shown below. The biofilter removed approximately
70 percent of the ammonia and 87 percent of the hydrogen sulfide in the gas stream. The biofilter also
eliminated all odors from the swine CAFO’s off-gas.
Biofilter treatment results during the 6-month pilot test
Pollutant

Influent loading
(lbs/day)

Gas flow
(cfm)

Ammonia

80

23,000

Hydrogen Sulfide

10

23,000

Effluent loading
(lbs/day)
25
1.3

Odor
None
None

Conclusion: Comparison of the pilot-scale testing results with the calculated overflow discharges indicates
the proposed treatment system cannot achieve a quantity of pollutants discharged for all the targeted
pollutants that is equal to or less than the quantity of pollutants that would be discharged under the baseline
performance standards. Because the proposed treatment system cannot achieve the reduction for all target
pollutants, the permitting authority denies the facility’s request for an individual NPDES permit for operation
and discharge of water from the proposed treatment system. If modifications to the treatment system can be
made that lower the annual discharge of phosphorus, an individual permit might be considered.
KFP has still decided to install a new biofilter system to remove odors, ammonia, and hydrogen sulfide from
its air stream to address complaints from neighbors regarding smells from the facility.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

F-19

NPDES Permit Writers’ Manual for CAFOs

Example 3. Birvan Egg Farms, Okeechobee County, Florida
Background
Birvan Egg Farms (Birvan) is a Large CAFO in Okeechobee County, Florida. Birvan has 40,000 laying hens
with an average weight of approximately 3 pounds. Birds are housed in a high-rise cage system. Manure
drops from the cages to the floor below and is picked up by the wet flush system and transferred to the
anaerobic digester. The anaerobic digester removes the majority of nutrients, BOD5, and volatile solids
while generating methane that is used in the facility’s boiler system. Effluent from the anaerobic digester is
pumped through a vibrating membrane filtration system for polishing residual solids, BOD5, and nutrients
before land application of the polished water to a small grass field. All solids are hauled and sold off-site.
Birvan elected to install an anaerobic treatment system rather than a holding pond because of space
constraints and the lack of crop land to apply liquids and solids. The manure treatment system has been in
operation since 1996.
Birvan calculated the overflow volume and loading from a baseline system (a liquid storage structure) that
could have been installed at the facility and compared the results with the loadings being obtained from the
existing treatment system.

Summary of baseline overflow volume and pollutant loading calculations
Estimated Storage Lagoon Volume if
Constructed:

58,200 ft 3 (435 thousand gallons)

Process Wastewater Generation:

374 ft 3/day (2,800 gal/day)

Volume of Liquids and Solids in Lagoon at Start: 635 ft 3 (Sludge Volume + Minimum Treatment Volume +
Accumulated Process Wastes Since Last Liquid Application)
Precipitation Volume (average):

61 in/yr

Evaporation Rate (average):

90 in/yr

Sludge Volume (constant):

5,900 ft 3

Minimum Treatment Volume (constant):

9,200 ft 3

Assumed removal rate:

2x per month from January 21 to December 9

Daily Accumulation of Lagoon Liquids (ft 3/day) = Process Waste (ft 3/day) + [Precipitation - Evaporation
(ft/day)] x Lagoon Surface Area (ft 2)
Volume of Lagoon Liquids (ft3) =

Previous Days’ Volume (ft 3) + Accumulation Volume
(ft 3/day)

Calculated baseline overflow volume method
Daily Accumulation of Lagoon Liquids (ft3/day) = Process Waste (ft3/day) + [Precipitation - Evaporation
(ft/day)] x Lagoon Surface Area (ft2)
Volume of Lagoon Liquids (ft3) = Previous Days’ Volume (ft3) + Accumulation Volume
(ft3/day)

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

F-20

NPDES Permit Writers’ Manual for CAFOs

Example 3. Birvan Egg Farms, Okeechobee County, Florida (continued)
If the Volume of Lagoon Liquids (ft 3) is greater than the following:
Existing Storage Lagoon Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment Volume (ft3)], then
Overflow Volume = Volume of Lagoon Liquids (ft 3) - [Existing Storage Lagoon
Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment
Volume (ft 3)]; and
Volume of Lagoon Liquids (ft 3) is adjusted to the following:
[Existing Storage Lagoon Volume (ft 3) - Sludge Volume (ft 3) - Minimum Treatment Volume (ft 3)] (the
maximum volume of liquids the lagoon can store)
Calculated Overflow Volume for Birvan 3,162 ft 3/yr (23,651 gal/yr)
Birvan collected a representative sample of liquid from the digester to calculate the annual loading of
BOD5, total N, total P, and TSS that would be discharged as a result of the overflow volume. The sample
was collected from the top 12 inches of the digester surface because the majority of overflows will likely be
attributed to this zone. The sampling results are shown below:
BOD5:

1,500 mg/L

Total N:

750 mg/L

Total P:

100 mg/L

TSS:

3,200 mg/L

On the basis of the overflow and the measured concentration, the annual pollutant discharges from the
storage system was calculated by multiplying the flow by the concentration as shown in the example for
BOD5 below:
BOD5: 1,500 mg/L x 3.785 L/gal x 23,651 gal/yr x 2.2 lbs/kg x 1 kg/10 6 mg = 295 lbs/yr
A summary of the pollutant loadings based on the overflow rate and concentration is shown below.
BOD5:

295 lbs/yr

Total N:

148 lbs/yr

Total P:

20 lbs/yr

TSS:

433 lbs/yr

Treatment system evaluation
Birvan has been collecting monthly samples for BOD5, total N, total P, and TSS from the existing treatment
system since early 1997. The measured monthly concentrations in the treatment system effluent and the total
flow through the treatment system over the past 12 months are shown below.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

F-21

NPDES Permit Writers’ Manual for CAFOs

Example 3. Birvan Egg Farms, Okeechobee County, Florida (continued)
Measured treatment system effluent concentration and total influent flow during
the past 12 months
BOD5
(mg/L)

N
(mg/L)

P
(mg/L)

TSS

Total flow
(gal)

June

20

3.3

0.6

14

83,800

July

21

5.2

0.8

15

83,200

August

13

1.6

0.7

10

84,600

September

8

0.8

0.6

9

83,900

October

9

0.6

0.4

7

84,200

November

18

3.5

0.6

13

84,700

December

13

2

0.7

11

84,300

Month

January

6

0.7

0.4

9

82,900

February

8

0.7

0.4

8

83,900

March

19

1.8

0.8

13

84,700

April

20

4.2

1.2

15

85,100

May

7

2.7

0.8

14

84,300

13

1.9

0.6

12

84,250

Median

As shown in the figure below, the vibrating membrane filter generates a concentrated wastestream equaling
20% of the influent flow (16,850 gal/month). That concentrated wastestream is sent to a 10,000-gallon
holding tank before off-site shipment. Effluent from the vibrating membrane filter enters a lift station where
submersible pumps transfer approximately 45,000 gallons per month back to the layer house for manure
flushing. According to a measured average flow rate of approximately 22,400 gallons per month at Outfall
001 and the concentration of pollutants in the vibrating membrane treatment system effluent, the following
annual loadings to St. Lucie Canal were calculated and compared to the baseline overflow loadings.
Comparison of the Calculated Baseline Overflow Discharge to the Treatment System Discharge
Pollutant

Baseline overflow (lbs/yr)

Treatment system discharge (lbs/day)

BOD5:

295

29

Total N:

148

4.2

Total P:

20

1.3

433

27

TSS:

Conclusion: The comparison shows that the existing treatment systems consisting of an anaerobic digester
and vibrating membrane filtration system achieve better performance than the baseline system for all
targeted pollutants. If water quality constraints for fecal coliform in the St. Lucie Canal make additional
treatment necessary, Birvan is also considering increasing the temperature of the digester to make it
thermophilic, a practice known to reduce fecal coliform in the effluent.

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

F-22

NPDES Permit Writers’ Manual for CAFOs

Example 3. Birvan Egg Farms, Okeechobee County, Florida (continued)

Diagram of existing treatment system
Fresh Water

Flush
water
tank

Birvan Egg Farm
Wet Layer House with High-Rise Cages

Cold Water
Boiler

Hot Water

Total Birds: 40,000
84,250 gal/month
Recycle Flush Water:
45,000 gal/month

Effluent Lift
Station

Digestive Gas
(methane and
carbon dioxide)

Vibrating
Membrane
Filter
Anaerobic
Digester

NPDES Outfall 001

Flow: 22,400 gal/month
BOD5: 2.4 lbs/month
Total Nitrogen: 0.18 lbs/month
Total Phosphorus: 0.05 lbs/month
TSS: 2.2 lbs/month

Membrane Concentrate:
16,850 gal/month

Concentrate
Storage
Tank

Contract Haul (2x/month)

(10,000 gal)

Birvan Egg Farm
Okeechobee County, FL

Appendix F: Voluntary Alternative Performance Standards for CAFOs
C. Step-By-Step Requirements for Participation in the Voluntary Performance Standards Program

NPDES Permit Writers’ Manual for CAFOs

Appendix
Winter Spreading
Technical Guidance

G

NPDES Permit Writers’ Manual for CAFOs

G-1

NPDES Permit Writers’ Manual for CAFOs

Interim Final

Technical Guidance
for the
Application of CAFO Manure on Land in the Winter
Water Division
Region 5
United States Environmental Protection Agency

Introduction1
Many owners or operators of concentrated animal feeding operations (CAFOs) use their manure,
litter, and process wastewater (hereinafter manure) as a source of nutrients for the growth of crops
or forage or to improve the tilth of soil. Others dispose of manure on land. The longer manure
remains in the soil before plants take the nutrients up, the more likely those nutrients will be
lost through volatilization, denitrification, leaching to subsurface drainage tile lines or ground
water, and runoff to surface water. To use the greatest fraction of the nutrients in manure, late
spring and early summer are the best times for land application. Some CAFO owners or operators
apply manure on land in the late fall or winter because crops are not growing, labor is available,
and, when it is frozen, the soil is able to handle the weight of manure hauling equipment without
excessive compaction. Application in the late fall or winter also enables the owner or operator
to avoid the cost of the structures that would be needed to store manure through the winter
months. From the dual perspectives of nutrient utilization and pollution prevention, however,
winter is the least desirable time for land application. Appendix G-1 contains an excerpt from the
U.S. Environmental Protection Agency (EPA) (2002 p. 177–78) summarizing the literature on the
risk that land application in the winter poses to water quality.
Under regulations that EPA promulgated in 2003, agencies that are authorized to issue National
Pollutant Discharge Elimination System permits (hereinafter states) need to have technical
standards for nutrient management that address, among other factors, the times at which CAFOs
may apply manure on land (see Title 40 of the Code of Federal Regulations [CFR]part 123.36).
Technical standards are to achieve realistic crop or forage production goals while minimizing
movement of nitrogen and phosphorus to waters of the United States. They will form the basis
for the nutrient management plans that CAFO owners and operators will implement under
40 CFR parts 122.42, 412.4.
EPA recognizes certain times during which there could be an increased likelihood that runoff
from CAFO land application areas could reach waters of the United States. The times include,
among others, when the soil is frozen or covered with ice or snow. Frozen soil will occur in areas
where snow or other ground cover is shallow and where prolonged periods of subfreezing air
temperatures prevail (U.S. Army Corps of Engineers 1998). The January normal daily minimum
air temperature in EPA Region 5 ranges from minus 8 degrees Fahrenheit (°F) in the northwest

Appendix G. Winter Spreading Technical Guidance

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NPDES Permit Writers’ Manual for CAFOs

to 22 °F in the south. Thus, all areas in the region are subject to air temperatures that can cause
soil to freeze. For December through March, the mean precipitation in the region ranges from
3 inches of water in the northwest to 14.6 inches of water in the south. The mean snowfall in those
months ranges from 13 inches in the south to 108 inches in the coastal north. The above normals
notwithstanding, the only reliable way to predict temperature and precipitation before any winter
is through statistical analysis of historical data for the location of interest.
To ensure effective implementation of the regulations, EPA (2003) has expressed its strong
preference that states prohibit the discharge of manure from land application. That is applicable
unless the discharge is an agricultural stormwater discharge (i.e., a precipitation-related
discharge from land where manure was applied in accordance with a nutrient management
plan). EPA has also expressed its strong preference for the way in which states in their technical
standards should address the timing of land application. With regard to the winter months, EPA
strongly prefers that technical standards either prohibit surface application on snow, ice, and
frozen soil or include specific protocols that CAFO owners or operators, nutrient management
planners, and inspectors will use to conclude whether application to a frozen or snow- or icecovered field, or a portion thereof, poses a reasonable risk of runoff. Where there is a reasonable
risk, EPA strongly prefers that technical standards prohibit application on the field or the
pertinent portion thereof during times when the risk exists or could arise.

Technical Guidance
This paper presents technical guidance to which EPA Region 5 will refer as we work together with
those states that plan to allow CAFO owners or operators to apply manure on land in the winter
where a crop will not be grown in that season or nutrients need not be applied in the winter to
grow the crop. For that purpose, Region 5 assumes that the risk of runoff will be minimized if a
state requires injection or timely incorporation of manure in the winter, provided that the CAFO
owner or operator adheres to the setback requirements in 40 CFR part 412.4(c)(5). Further, we
assume that the risk of runoff will be minimized if waters of the United States, sinkholes, open
tile line intake structures, and other conduits to waters of the United States are upslope from the
land on which manure would be surface applied. Thus, the balance of this technical guidance
is intended to provide a basis for the region to evaluate the adequacy of preliminary technical
standards that would allow surface application without timely incorporation where waters of the
United States, sinkholes, open tile line intake structures, or other conduits to waters of the United
States are downslope from the land on which the manure would be applied.2

Potential Discharges That Are Not Precipitation Related
When liquid manure is applied on frozen soil in the absence of snow cover, Region 5 has
concluded that the manure will run off and potentially discharge if it is applied in excess of the
pertinent rate specified in Table G-1a or G-1b.3 For an example that shows how the region came to
this conclusion, see Appendix G-2. In as much as the discharge of manure is not an agricultural
stormwater discharge when it is not related to precipitation, technical standards need to prohibit
the application of liquid manure on frozen soil, in excess of the rates provided in the following
tables, when the soil is not covered with snow.

Appendix G. Winter Spreading Technical Guidance

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NPDES Permit Writers’ Manual for CAFOs

Liquid Manure Maximum Rates of Application onto Frozen Soil
Table G-1a. Harvested Crops were row crops planted in straight rows with land in
good hydrologic condition
Hydrologic Soil Group*

Maximum rate of application
(gallons per acre)

A

3,000

B

1,600

C

1,100

D

1,100

Table G-1b. Harvested crops were close-seeded legumes planted in straight rows
with land in good hydrologic condition
Hydrologic Soil Group

Maximum rate of application
(gallons per acre)

A

4,100

B

2,200

C

1,100

D

1,100

*See Appendix A of U.S. Department of Agriculture, Soil Conservation Service (1986) for information
on the Hydrologic Soil Group within which a given soil is classified. The appendix is at ftp://ftp.wcc.nrcs.
usda.gov/wntsc/H&H/other/TR55documentation.pdf.

Discharges That Are Precipitation Related
When manure is applied on land in the winter, Region 5 assumes that nutrients and manure
pollutants will dissolve or become suspended in any precipitation that comes into contact with
the manure. That assumption is consistent with the findings reported in Appendix G-1 and
Table G-2. The technical guidance that follows is intended to provide a basis for the region to
evaluate the adequacy of preliminary technical standards as such standards affect the movement
of nutrients and manure pollutants in precipitation runoff during the winter or early spring. Six
substantive steps are presented below. The first three involve the formulation of state policy for
nutrient management. As contemplated in Step 1, the policy should include a standard for the
concentration or mass of biochemical oxygen demand (BOD) in precipitation-related discharges.
Nutrients, including ammonia and nitrite, contribute to that demand. The final three involve
engineering analysis to determine whether the BOD standard will be met.
Step 1: In collaboration with Region 5, the state establishes a standard for the concentration
or mass of BOD that will be permitted in precipitation-related discharges from land on
which manure has been surface applied in the winter.

Appendix G. Winter Spreading Technical Guidance

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NPDES Permit Writers’ Manual for CAFOs

Table G-2. Assumed initial concentration of bod in runoff from land on which
manure or process wastewater has been surface applied
Type of material
Broiler manurea

Initial total BOD in runoff
(mg/L)
708

Cattle (other than manure dairy cow) manure

Reserved

Cattle open lot process wastewater

Reserved

Egg wash process wastewater

Reserved

Feed storage process wastewater

Reserved

Layer manureb

809

Mature dairy cow manurec

924

Swine manured

204

Turkey manure

Reserved

Daniel et al. 1995
Ibid.
c Thompson et al. 1979
d Daniel et al. 1995
a

b

Step 2: A. The state establishes preliminary technical standards for the setback4 and the type,
form, and maximum quantity of manure that could be surface applied on land in the
winter. Standards for the setback should be expressed in terms of distance and slope.
The minimum distance is that required under 40 CFR part 412.4(c)(5). As required to use
equations 2 or 3, below, standards for the setback should also be expressed in terms of the
land cover and treatment practice and the crop residue rate (in the case of equation 2) or
the Hydrologic Soil Group (in the case of equation 3). For information on various residue
rates and land cover and treatment practices, see Tables G-3 and G-4.

B. If the standard established in Step 1 is expressed as a mass, the state establishes
additional preliminary technical standards for the land cover and treatment practice and
Hydrologic Soil Group applicable to land that is upslope from the setback.

Step 3: So that Region 5 can perform the engineering analysis, the state establishes appropriate
design conditions for the land use, form of precipitation (rain or ripe snow), depth
of precipitation, and the temperature and moisture content of soil. At a minimum,
the design condition for the moisture content of soil should be antecedent moisture
condition III (i.e., saturated soil) (Wright 2004; Linsley et al. 1982). States should carefully
review climate data to determine whether the design temperature of soil should be
0 degrees Celsius (°C) or less. In no case should the design temperature of soil exceed 3 °C.

Appendix G. Winter Spreading Technical Guidance

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Table G-3. Recommended Manning’s roughness coefficients for overland flow
Recommended
coefficient

Range

Bare clay-loam (eroded)

0.02

0.012 to 0.033

Fallow - no residue

0.05

0.006 to 0.16

< 0.25

0.07

0.006 to 0.17

0.25 to 1

0.18

0.07 to 0.34

1 to 3

0.3

0.19 to 0.47

>3

0.4

0.34 to 0.46

< 0.25

0.08

0.008 to 0.41

0.25 to 1

0.16

0.1 to 0.25

1 to 3

0.25

0.14 to 0.53

Cover or treatment

Chisel plow

Disk/harrow

Residue rate
(ton/acre)*

>3

0.3

--

< 0.25

0.04

0.03 to 0.07

0.25 to 1

0.07

0.01 to 0.13

1 to 3

0.3

0.16 to 0.47

Moldboard plow (fall)

0.06

0.02 to 0.1

Coulter

0.1

0.05 to 0.13

Range (natural)

0.13

0.02 to 0.32

Range (clipped)

0.1

0.02 to 0.24

Short grass prairie

0.15

0.1 to 0.2

Dense grass

0.24

0.17 to 0.3

No till

Source: Engman 1986
* See Figure G-2 to convert residue cover from a percent to a mass.

Appendix G. Winter Spreading Technical Guidance

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NPDES Permit Writers’ Manual for CAFOs

Figure G-1. Average velocity of shallow concentrated flow. (Source: USDA NRCS 1993)

Figure G-2. Pounds of residue vs. percent ground cover. (Source: USDA NRCS 2002b)

Appendix G. Winter Spreading Technical Guidance

G-7

NPDES Permit Writers’ Manual for CAFOs

Table G-4. Runoff curve numbers for hydrologic soil-cover complexesa

Land use
Fallow

Row crops

Small grain

Close-seeded legumesc
or rotation meadow

Treatment or practice

Hydrologic
conditionb

Bare soil

Hydrologic soil
group
A

B

C

D

89

94

97

98

Crop residue cover

Poor

89

94

96

98

"

Good

88

93

95

96

Straight row

Poor

86

92

95

97

"

Good

83

90

94

96

Straight row and cop residue
cover

Poor

86

91

95

96

"

Good

81

88

92

94

Contoured

Poor

85

91

93

95

"

Good

82

88

92

94

Contoured and crop residue

Poor

84

90

93

95

"

Good

81

88

92

94

Contoured and terraced

Poor

82

88

91

92

"

Good

79

86

90

92

Contoured, terraced, and crop
residue

Poor

82

87

91

92

"

Good

78

85

89

91

Straight row

Poor

82

89

93

95

Contoured

Poor

80

88

92

94

"

Good

78

87

92

93

Contoured and crop residue

Poor

79

87

92

93

"

Good

78

86

91

93

Contoured and terraced

Poor

78

86

91

92

"

Good

77

85

90

92

Contoured, terraced, and crop
residue

Poor

78

86

90

92

"

Good

76

84

89

91

Straight row

Poor

82

89

94

96

"

Good

76

86

92

94

Appendix G. Winter Spreading Technical Guidance

G-8

NPDES Permit Writers’ Manual for CAFOs

Table G-4. Runoff curve numbers for hydrologic soil-cover complexesa (continued)

Land use

Close-seeded legumesd
or rotation meadow

Hydrologic soil
group

Treatment or practice

Hydrologic
conditionb

A

B

C

D

Contoured

Poor

81

88

93

94

"

Good

74

84

90

93

Contoured and terraced

Poor

80

87

91

93

"

Good

70

83

89

91

Poor

84

91

94

96

Fair

69

84

91

93

Good

59

78

88

91

Contoured

Poor

67

83

92

95

"

Fair

43

77

88

93

"

Good

13

55

85

91

Good

50

76

86

90

Pasture or range

Meadow
Source: USDA NRCS 1993; USDA SCS 1986

The runoff curve numbers in this table apply to saturated soil conditions (i.e., antecedent moisture condition III).
For runoff curve numbers applicable to average soil moisture conditions, see Appendix G-3.
a

b According to USDA SCS (1986), hydrologic condition is based on a combination of factors, including (a) density
and canopy of vegetative areas, (b) amount of year-round cover, (c) amount of grass or close-seeded legumes in
rotation, (d) percent of residue cover on the land surface (good ≥ percent), and (e) degree of surface roughness.
c

Close-drilled or broadcast

d

Close-drilled or broadcast

Step 4: The region calculates the percent removal of BOD that will occur in the setback, given the
design conditions and preliminary technical standards. Calculating the percent removal
is a two-step process, as shown in A and B below.

A. Calculate the amount of time it takes water to travel or concentrate (Tc) across the
setback distance. Two equations are provided below as options for calculating Tc. In
general, use equation 1 (USDA NRCS 2002a) when the design condition consists of
rain on frozen soil or rain on ripe snow or when the preliminary technical standards
specify a residue rate equal to or greater than 20 percent. Use equation 3 (USDA NRCS
1993) when the design condition consists of ripe snow, the preliminary technical
standards do not specify a residue rate, or the rate is less than 20 percent.

Appendix G. Winter Spreading Technical Guidance

G-9

NPDES Permit Writers’ Manual for CAFOs

Eq. 1

Tc (hr) = Tt (overland) + Tt (shallow concentrated)

where

Eq. 2

Tt (overland) =

0.007 × (N × L)0.8
(P 0.5) × (x0.4)

N = Manning’s roughness coefficient for overland flow. To select a coefficient
that is appropriate in light of the preliminary technical standards, see
Table G-3.
L = overland flow portion of the setback distance (maximum of 100 feet) (ft).
P = precipitation design depth (in).
s = preliminary technical standard for the slope over the distance L (ft/ft).

Tt (shallow concentrated) applies to the shallow concentrated flow portion of the setback distance.
In other words, it applies to the portion that is between points (a) and (b) as described
below.

Point (a): 100 feet downslope from the furthest downslope point at which manure would
be applied under the preliminary technical standards.

Point (b): the nearest waters of the United States, sinkhole, open tile line intake structure,
or other conduit to waters of the United States. Tt (shallow concentrated) is determined by
multiplying the above distance times a velocity of runoff that is appropriate in light of the
preliminary technical standards. See Figure G-1.
Eq. 3

Tc (hr) =

where

(L0.8) × (S + 1)0.7
5
×
1900 × (s0.5)
3

L = preliminary technical standard for the setback distance (ft).
S = potential maximum retention after runoff begins

= (1,000 / CN) – 10

CN = runoff curve number. To select a number that is appropriate in light
of the design condition for the land use and the preliminary technical
standards, see Table G-3.
s = preliminary technical standard for the slope over the distance L
(percent).

Appendix G. Winter Spreading Technical Guidance

G-10

NPDES Permit Writers’ Manual for CAFOs

B. Calculate the percent removal of BOD in the setback. The equation for percent removal
is as follows (modified from Martel et al. 1980):
Eq. 4

E = (1 – A × e–(kT)×t) × 100

where
E = percent removal of BOD
A = nonsettleable fraction of BOD in manure

= 0.5 to 0.6 for animals other than mature dairy cows (Zhu 2003)

= 0.9 for mature dairy cows (Wright 2004)

kT = first-order reaction rate constant at the design temperature of soil (T) (°C)

= k × (Θ)T-20

Θ = 1.135 (Schroepfer et al. 1964)
k = 0.03/min5
t = detention time

= Tc × 60

Step 5: Region 5 multiplies the percent removal calculated in Step 4. B. times the initial
concentration of BOD in runoff from land where manure has been surface applied
(i.e., the concentration before treatment of the runoff by land in the setback). If statespecific data are not available, use the values from Table G-2 as the basis for assumptions
about the initial concentration. Subtract from the initial concentration the product
of the percent removal times the initial concentration. If the standard established in
Step 1 is expressed as a mass, proceed to Step 6. If it is expressed as a concentration,
compare the final concentration to the standard. If the final concentration is less than
or equal to the standard, the region will conclude that there is no reasonable risk of
runoff. The region will neither object to nor disapprove the state’s preliminary technical
standards. However, for the analysis to hold, the technical standards need to require
the CAFO owner or operator to verify that conditions in the setback at the beginning
of any application are consistent with the values assigned to N or S. In other words, the
standards need to prohibit surface application when ice reduces the surface roughness
or occupies the surface storage in the setback. If the concentration is greater than the
standard established in Step 1, the region will conclude that there is a reasonable risk of
runoff. Therefore, the final technical standards need to prohibit surface application of
manure in the winter (or on frozen or snow-covered soil) or the state needs to otherwise
strengthen the preliminary technical standards so there is no reasonable risk of runoff.

Appendix G. Winter Spreading Technical Guidance

G-11

NPDES Permit Writers’ Manual for CAFOs

Step 6: If the standard is expressed as a mass, Region 5 calculates the mass of BOD that will
run off the land given the design conditions for the land use, depth of precipitation, soil
temperature, and soil moisture content and the preliminary technical standards for the
Hydrologic Soil Group, land cover and treatment practice, and the type and maximum
quantity of liquid manure. Calculating the mass is a three-step process as shown below.

A. Use the following equation (USDA NRCS 1993) to calculate the inches of runoff.
(P - 0.2 × S)2
(P + 0.8 × S)

Eq. 5

Q=

where
Q = runoff (in)
P = precipitation design depth plus the depth of water that could be applied
in the winter as liquid manure given the preliminary technical standards
(in).
S = the same as defined for equation 3 except that, if the design temperature
of soil is 0 °C or less, substitute Sf for S where Sf = (0.1 × S)
(Mitchell et al. 1997).

B. Use the following equation to convert the runoff from inches to a volume per acre.
Eq. 6

C. Calculate the mass of BOD in runoff by multiplying the volume of runoff times the final
concentration of BOD calculated in Step 5. The equation is as follows:
Eq. 7

Q (gal/ac) = Q (in) × ft/12 in × 43,560 ft2/ac × 7.48 gal/ft3

BOD (lb/ac) = BOD (mg/l) × Q (gal/ac) × 3.7854 L/gal × g/1000 mg × 0.0022 lb/g

Compare the mass with the standard established in Step 1. If the mass is less than
or equal to the standard, Region 5 will conclude that there is no reasonable risk of
runoff. The region will neither object to nor disapprove the preliminary technical
standards. However, for the analysis to hold, the technical standards need to require
the CAFO owner or operator to verify that conditions in the setback at the beginning
of any application are consistent with the values assigned to N or S. In other words, the
standards need to prohibit surface application when ice reduces the surface roughness
or occupies the surface storage in the setback. If the mass is greater than the standard
established in Step 1, Region 5 will conclude that there is a reasonable risk of runoff.
Therefore, the final technical standards need to prohibit surface application of manure in
the winter (or on frozen or snow-covered soil) or the state needs to otherwise strengthen
the preliminary technical standards so there is no reasonable risk of runoff.

Appendix G. Winter Spreading Technical Guidance

G-12

NPDES Permit Writers’ Manual for CAFOs

References
Daniel, T., D. Edwards, and D. Nichols. 1995. Edge-of-field losses of surface-applied animal
manure. In Animal Waste and the Land-Water Interface, ed. K. Steele. CRC Press,
Boca Raton, FL.
Engman, E.T. 1986. Roughness coefficients for routing surface runoff. Journal of Irrigation and
Drainage Engineering 112:39–53.
Linsley, R., M. Kohler, and J. Paulhus. 1982. Hydrology for Engineers. McGraw-Hill, New York.
Martel, C., D. Adrian, T. Jenkins, and R. Peters. 1980. Rational design of overland flow systems. In
Proceedings of the ASCE National Conference on Environmental Engineering. American Society
of Civil Engineers, Reston, VA.
Mitchell, G., R. Griggs, V. Benson, and J. Williams. 1997. Environmental Policy Integrated Climate
(EPIC) User’s Manual. U.S. Department of Agriculture, Agricultural Research Service,
Temple, TX.
Schroepfer, G., M. Robins, and R. Susag. 1964. The research program on the Mississippi River
in the Vicinity of Minneapolis and St. Paul. In Advances in Water Pollution Research, vol. 1.
Pergamon. London, England.
Thompson, D., T. Loudon, and J. Gerrish. 1979. Animal manure movement in winter runoff for
different surface conditions. In Best Management Practices for Agriculture and Silviculture,
Proceedings of the 1978 Cornell Agricultural Waste Management Conference, eds. R. Loehr,
D. Haith, M. Walter, and C. Martin. Ann Arbor Science Publishers, Ann Arbor, MI.
U.S. Army Corps of Engineers. 1998. Engineering and Design—Runoff from Snowmelt. EM 1110-21406. U.S. Army Corps of Engineers, Washington, D.C.
USDA NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service). 1993.
National Engineering Handbook, Part 630, Hydrology. U.S. Department of Agriculture,
Washington, D.C.
USDA NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service). 2002a.
Urban Hydrology for Small Watersheds. Technical Release 55 (WinTR-55). U.S. Department of
Agriculture, Washington, D.C.
USDA NRCS (U.S. Department of Agriculture, Natural Resources Conservation Service). 2002b.
Residue Management Seasonal (Acre). Conservation Practice Standard 344. U.S. Department of
Agriculture, Des Moines, IA.
USDA SCS (United States Department of Agriculture, Soil Conservation Service—now NRCS).
1986. Urban Hydrology for Small Watersheds. Technical Release 55. U.S. Department of
Agriculture Soil Conservation Service, Washington, D.C.

Appendix G. Winter Spreading Technical Guidance

G-13

NPDES Permit Writers’ Manual for CAFOs

U.S. Environmental Protection Agency. 2003. NPDES Permit Writers’ Guidance Manual and
Example NPDES Permit for Concentrated Animal Feeding Operations. EPA-833-B-04-001.
U.S. Environmental Protection Agency, Washington, D.C.
U.S. Environmental Protection Agency. 2002. Development Document for the Final Revisions
to the National Pollutant Discharge Elimination System Regulation and Effluent
Limitations Guidelines for Concentrated Animal Feeding Operations. EPA-821-R-03-001.
U.S. Environmental Protection Agency, Washington, D.C.
U.S. Environmental Protection Agency. 2000. Peer Review Handbook, 2nd ed. EPA 100-B- 00-001.
U.S. Environmental Protection Agency, Washington, D.C.
Wright, P. 2004. Letter to Steve Jann, EPA, Region 5. Cornell Cooperative Extension, Ithaca, NY.
Zhu, J. 2003. Personal communication with Steve Jann, EPA, Region 5. University of Minnesota,
Southern Research and Outreach Center, Waseca, MN.

Endnotes
In accordance with the U.S. Environmental Protection Agency (2000), Region 5 asked three professional engineers
to review a February 2004 draft of this document. The peer review record includes responses to the comments that
those individuals provided pursuant to the request.

1

For the purpose of this technical guidance, “other conduits to waters of the United States” means any area wherein
water is or could be conveyed to waters of the United States via channelized flow.

2

Region 5 developed the tables for the corn and soybean crops commonly grown in the region. On request, the
region can supply tables for other land uses and land cover and treatment practices.

3

The term setback is defined in 40 CFR part 412.4 to mean a specified distance from surface waters (i.e., waters of the
United States) or potential conduits to surface waters where manure may not be land applied.

4

The k value of 0.03 per minute is as reported by Martel et al. (1980) for treatment of municipal wastewater by the
overland flow process. The region assumes that Martel et al., reported the constant at 20 °C consistent with standard
engineering practice.

5

Appendix G. Winter Spreading Technical Guidance

G-14

NPDES Permit Writers’ Manual for CAFOs

Appendix G-1
The following is an excerpt from EPA (2002 p. 177–78):
[C]onsiderable research has demonstrated that runoff from manure application on
frozen or snow-covered ground has a high risk of water quality impact. Extremely
high concentrations of nitrogen and phosphorus in runoff have been reported from
plot studies of winter-applied manure: 23.5 to 1,086 milligrams (mg) of total Kjeldahl
nitrogen (TKN) per liter (L) and 1.6 to 15.4 mg/L of phosphorus (P) (Thompson, et al.
1979; Melvin and Lorimor 1996). In two Vermont field studies, Clausen (1990, 1991)
reported 165 to 224 percent increases in total P concentrations, 246 to 1,480 percent
increases in soluble P concentrations, 114 percent increases in TKN concentrations,
and up to 576 percent increases in ammonia-nitrogen (NH3-N) following winter
application of dairy manure. Mass losses of up to 22 percent of applied nitrogen and up
to 27 percent of applied P from winter-applied manure have been reported (Midgeley
and Dunklee 1945; Hensler et al. 1970; Phillips et al. 1975; Converse et al. 1976; Klausner
et al. 1976; Young and Mutchler 1976; Clausen 1990, 1991; Melvin and Lorimor 1996).
Much of this loss can occur in a single storm event (Klausner et al. 1976). Such losses
could represent a significant portion of annual crop needs.
On a watershed basis, runoff from winter-applied manure can be an important source
of annual nutrient loadings to waterbodies. In a Wisconsin lake, 25 percent of annual P
load from animal waste sources was estimated to arise from winter spreading (Moore
and Madison 1985). In New York, snowmelt runoff from winter-manured cropland
contributed more P to Cannonsville Reservoir than did runoff from poorly managed
barnyards (Brown et al. 1989). Clausen and Meals (1989) estimated that 40 percent of
Vermont streams and lakes would experience significant water quality impairments
from the addition of just two winter-spread fields in their watersheds.
Winter application of manure can increase microorganism losses in runoff from
agricultural land compared to applications in other seasons (Reddy et al. 1981). Cool
temperatures enhance survival of fecal bacteria (Reddy et al., 1981; Kibby et al. 1978).
Although some researchers have reported that freezing conditions are lethal to fecal
bacteria (Kibby et al. 1978; Stoddard et al. 1998), research results are conflicting. Kudva
et al. (1998) found that Escherichia coli can survive more than 100 days in manure
frozen at minus 20 degrees Celsius. Vansteelant (2000) observed that freeze/thaw of
soil/slurry mix only reduced E. coli levels by about 90 percent. Studies have found that
winter spreading of manure does not guarantee die-off of Cryptosporidium oocysts
(Carrington and Ransome 1994; Fayer and Nerad 1996). Although several studies
have reported little water quality impact from winter-spread manure (Klausner 1976;
Young and Mutchler 1976; Young and Holt 1977), such findings typically result from
fortuitous circumstances of weather, soil properties, and timing/position of manure in
the snowpack. The spatial and temporal variability and unpredictability of such factors
makes the possibility of ideal conditions both unlikely and impossible to predict.

Appendix G-1.

G-15

NPDES Permit Writers’ Manual for CAFOs

Appendix G-2. Example Derivation of the Maximum Rates for
Liquid Manure Application on Frozen Soil
Givens
According to USDA NRCS (1993), the following are givens:
Potential maximum retention after runoff begins (S)

=

1,000 – 10
CN

Runoff curve number (CN)

=

1,000
S + 10

According to Mitchell et al. (1997), the following is a given for frozen soil:
Sf = 0.1 × S
For CN in the range from zero to 100, Table 10.1 in USDA NRCS (1993), identifies the minimum
depth of precipitation (P) at which the runoff curve begins under dry, average, and saturated
antecedent soil moisture conditions. For example, for a CN of 91 and average antecedent soil
moisture, the runoff curve begins when P equals 0.2 inch.
Example
Hydrologic Soil Group A.
Harvested crop was corn planted in straight rows.
The land is in good hydrologic condition.
The antecedent soil moisture is average.
Sf

= (1,000 / 64 – 10) × 0.1 =

CNf = (1,000 / (0.56 + 10)

=

0.56
94.7  ≅  95

According to Table 10.1 in USDA NRCS (1993), for a CN of 95, 0.11 inch is the minimum depth of
precipitation (or other liquid) at which the runoff curve begins. Converting that depth to a volume
per acre,
Q (gal/ac) = 0.11 in × ft/12 in × 43,560 ft 2/ac × 7.48 gal/ft3
results in 2,987 gallons per acre as the maximum quantity of liquid that can be applied on frozen
soils in Hydrologic Soil Group A while precluding runoff.

Appendix G-2.

G-16

NPDES Permit Writers’ Manual for CAFOs

Appendix G-3. Runoff Curve Numbers for
Antecedent Moisture Condition II

Appendix G-3.

If the curve number for
AMC III is …

then the curve number for
AMC II is …

100
99
98
97
96
95
94
93
92
91
90
89
88
87
86
85
84
83
82
81
80
79
78
77
76
75
74
73
72
71
70
69
68
67
66
65
64
63
62
61

99
96
93
91
89
87
85
83
81
79
78
76
74
73
71
70
68
67
65
64
63
62
60
59
58
57
55
54
53
52
50
49
48
47
46
45
44
43
42
41

NPDES Permit Writers’ Manual for CAFOs

Appendix
NPDES CAFO Nutrient
Management Plan
Review Checklist

H

NPDES Permit Writers’ Manual for CAFOs

H-1

NPDES Permit Writers’ Manual for CAFOs

Introduction
This checklist is a tool to guide the review of a nutrient management plan (NMP) submitted with a
National Pollutant Discharge Elimination System (NPDES) permit application or notice of intent
(NOI). The checklist supports the permit writer’s determination of whether the NMP adequately
addresses each of the nine minimum practices required in the regulations. That determination
should be based on an assessment of the following for each minimum practice:
1. Are the practices and procedures identified in the NMP sufficient to prevent discharges
to surface water?
2. Are the practices and procedures adequate to support identification of NMP terms for
the permit?
The checklist is focused on the fundamental concepts necessary to evaluate whether an NMP
addresses the regulatory requirements (e.g., NPDES minimum standards and effluent limitations
guideline (ELG) requirements). The checklist is organized into three parts: (1) Part A – Basic
Facility Information, (2) Part B – Nine Minimum Practices and Associated Information, and
(3) Part C – Plan Adequacy. Associated information in Part B includes information associated with
each minimum practice and is used to help to determine if the plan meets the requirements of
the minimum practices. For example, crop information is necessary to review the protocols for
land application of manure and wastewater minimum practice.

Using the Checklist
The checklist has been designed to serve as a tool for use in determining whether an NMP
addresses the ELG requirements (where applicable) and NPDES NMP minimum practices. It
also addresses the information needed to identify the terms of an NMP as defined by EPA. The
checklist was designed to cover a variety of NMPs and operations; as such, it should cover most
common situations a permit writer will encounter. However, specific operational characteristics
can vary widely depending on animal sector, climate, state requirements, and other factors.
Permit writers should be aware of the characteristics of a typical CAFO in their area and, if
needed, revise the checklist to improve its utility in evaluating NMPs for a specific state or region.
Although the checklist is intended for use by permit writers in evaluating NMPs, the completed
checklist for a facility should be saved in the permit file and be made available as a reference
for the CAFO inspector to review before conducting a compliance inspection. The checklist
information would enable the inspector to document changes that have occurred at the operation
since the permit was issued and verify that they are reflected in the current NMP.
The determination of whether an NMP addresses the nine minimum practices often will be based
on best professional judgment. Even where a plan appears to address each of the nine minimum
practices, a poorly developed plan could be an indicator of a potential future permit violation.
Further, as described in Chapter 4 of this Manual, broadly applicable permit could be captured
as terms and conditions of the permit and therefore might not necessarily be addressed in the
operation’s NMP.

Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-2

NPDES Permit Writers’ Manual for CAFOs

NPDES CAFO NMP Nine Minimum Practices Review Checklist
Part A

Basic Facility Information

Documents location information and basic information about the type and size of the
operation.

Part B

Nine Minimum Practices

Documents critical information and terms specific to each of the NMP nine minimum
practices, including information associated with or necessary to review how the plan
addresses each practice.

Part C

Plan Adequacy

For use by the plan reviewer to document an overall determination of plan adequacy.

Note: Some of the information in the checklist might apply to Large CAFOs only. For additional details, consult the
regulations.

Part A – Basic Facility Information
1. Facility Identification


Operation Name:_____________________________________________________________



NPDES permit number:________________________________________________________

2. Plan Preparer Certification


Did the plan preparation involve certified technical specialists? ................................................  Yes

 No



Are the name and certification credentials of the plan preparer identified in the plan?..............  Yes

 No

3. Type of Operation


Is the operation

 Large CAFO



Is the operation

 Open lot

Notes:

 Medium or Small CAFO
 Partially enclosed

 Other (non-CAFO)

 Fully enclosed

_________________________________________________________________
_________________________________________________________________
_________________________________________________________________



Does the description of the facility in the plan reflect the description of the facility in the
application/NOI/fact sheet/permit? ............................................................................................  Yes

 No

4. Facility Location


Street Address (mailing):_______________________________________________________



City, State, ZIP:______________________________________________________________



Does the plan include maps that identify
(1) The location of the production area, including confinement areas, manure and
wastewater handling and storage areas, and raw material handling and storage
areas)? ........................................................................................................................  Yes

 No

(2) All land application areas owned or under the ownership, rental, lease, other legal
arrangement of the CAFO operator, including topography and soil types? .................  Yes

 No

(3) Environmentally sensitive areas (sinkholes, wells, drinking water sources, tile drain
outlets, etc.) for the production and land application areas? .......................................  Yes

 No



Does the plan identify the latitude and longitude to the entrance of the production area? ........  Yes

 No



Does the plan identify the watershed(s) in which the operation is located? ..............................  Yes

 No

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist
Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-3

H-3

NPDES Permit Writers’ Manual for CAFOs



Is the watershed listed on the state’s list of impaired watersheds? ...........................................  Yes

 No

If yes, what impairments are identified?_________________________________________
_________________________________________________________________
_________________________________________________________________


Is this facility within a state-designated source water protection area? .....................................  Yes
Are there any other water quality concerns in this watershed? .................................................  Yes

 No
 No

Explain: _________________________________________________________________
_________________________________________________________________
_________________________________________________________________

5. Animals


What type(s) of animals are confined at the facility?
 Beef (slaughter/feeder)
 Dairy
 Swine
 Turkey
 Duck



What is the maximum number of animals confined, by animal type?
 Beef (slaughter/feeder) __________
 Chicken – Layer _________________________
 Dairy ________________________
 Chicken – Broiler ________________________
 Swine _______________________
 Sheep/Lambs ___________________________
 Turkey _______________________
 Horse _________________________________
 Duck ________________________
 Other _________________________________



Is the plan based on the animal numbers listed above? ............................................................  Yes

 Chicken – Layer
 Chicken – Broiler
 Sheep/Lambs
 Horse
 Other __________________________________

 No

If no, on what capacity is the plan based?_______________________________________
_________________________________________________________________
_________________________________________________________________

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist

H-4

Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-4

NPDES Permit Writers’ Manual for CAFOs

Part B – Nine Minimum Practices
Minimum Practice: Ensure Adequate Storage Capacity
Manure/Litter/Process Wastewater Generation


What are the manure generation rates identified in the plan?
Animal Type 1:_______________________ ____________ lbs/year
Animal Type 2:_______________________ ____________ lbs/year
Animal Type 3:_______________________ ____________ lbs/year



Are the manure generation rates generally consistent with the USDA’s Agricultural Waste
Management Field Handbook? ...............................................................................................  Yes

 No

If no, are other practices in place that account for the rates included in the plan? ....................  Yes

 No

If yes, what are the practices identified in the plan? ...............................  Feed Management

 Other

Explain: __________________________________________________________
_________________________________________________________________


Does the plan identify all sources of process wastewater and appropriate generation rates? ..  Yes

 No

Storage Capacity


Does the plan identify the volume and number of days of storage required for the facility? ......  Yes

 No



Does the plan identify the size (in acres) of the production area? .................... Yes ________acres

 No



Does the plan identify the number and type of storage structures?...........................................  Yes

 No



Does the plan document the source of the information to calculate available storage volume?  Yes

 No



Does the storage volume in the plan account for manure and process wastewater generation
(including silage leachate and other wastes) during the storage period in addition to the
collection of runoff and direct precipitation on the surface of the storage structure from normal
precipitation and the design storm event (25-year, 24-hour storm or other as required/appropriate
for new source swine, poultry, and veal calf operations) for the CAFO location, a minimum
treatment volume for anaerobic lagoons, and volume for solids accumulation?........................  Yes

 No

Does the plan use the correct 25-year, 24-hour rainfall amount for the location of this operation
to determine storage requirements (or other storm event as required/appropriate for new
source swine, poultry, and veal calf operations)? ......................................................................  Yes

 No



Note source of information:____________________________________________________


Are the evaporation rates used in the plan consistent with local data/guidance and
appropriately applied? ...............................................................................................................  Yes

 No



Does the plan include a schedule for cleaning out the storage structures or solids removal
for liquid storage structures? .....................................................................................................  Yes

 No



Does the plan document that available storage volume is consistent with the plan’s specified
land application schedule? .......................................................................................................  Yes

 No



Does the plan require maintenance for all storage structures? .................................................  Yes

 No



Does the plan identify the specific maintenance actions and a frequency/schedule for
those actions? ...........................................................................................................................  Yes

 No

Terms for Minimum Practice: Ensure Adequate Storage Capacity (identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist
Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-5

H-5

NPDES Permit Writers’ Manual for CAFOs

Minimum Practice: Ensure Proper Management of Mortalities


Is the animal mortality addressed in the plan? ........................................................................  Yes
If yes, what methods are identified in the plan to address animal mortality?
 Rendering
 Incineration
 Composting
 Disposal pits
 Landfill
 Other_______________________________________

 No



Does the plan include a schedule for collecting, storing, and disposing of animal carcasses? .  Yes

 No



Does the plan address mortality storage before final disposition? .............................................  Yes

 No



Is the mortality rate used in the plan consistent with USDA expected values for the
animals confined at the operation? ............................................................................................  Yes

 No



Does the plan include contingency plans for unexpected but possible occurrences such as
mass mortality or the loss of a rendering contractor? ................................................................  Yes

 No



Does the animal mortality plan meet state and local requirements? ............................  N/A  Yes

 No

Terms for Minimum Practice: Ensure Proper Management of Mortalities (identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Minimum Practice: Divert Clean Water from Production Area


Does the plan address the diversion of clean water from the production areas?.......................  Yes

 No

If no, why?________________________________________________________________
__________________________________________________________________
If no, is the runoff being collected and is storage of runoff adequate?
(See the Minimum Practice: Ensure Adequate Storage Capacity section) ..................  Yes

 No

 Does the plan require periodic visual inspection to verify proper and functional diversion? ......  Yes

 No

 Does the plan address the maintenance of diversion structures? .............................................  Yes

 No

Terms for Minimum Practice: Divert Clean Water from Production Area (identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Minimum Practice: Prevent Direct Contact


Does the facility or topographic map identify any surface water in the production area? ..........  Yes

 No



If yes, are measures in the plan to prevent direct contact? .......................................................  Yes

 No



What are the measures identified in the plan?.................................................................  Fences



Does the plan address maintenance of the identified practices? ...............................................  Yes

 Other
 No

Terms for Minimum Practice: Prevent Direct Contact (identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist

H-6

Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-6

NPDES Permit Writers’ Manual for CAFOs

Minimum Practice: Chemical Disposal




Does the plan include practices that ensure chemicals (including pesticides, hazardous and
toxic chemicals, and petroleum products/by-products) are not disposed of in any storage or
treatment system that is not specifically designed to treat those chemicals? ............................  Yes

 No

Has the facility incorporated measures (in accordance with applicable laws and regulations)
to prevent mishandling of pesticides, hazardous and toxic chemicals, and petroleum
products/by-products? ...............................................................................................................  Yes

 No

If no, explain:_______________________________________________________________
______________________________________________________________________
Terms for Minimum Practice: Chemical Disposal (identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Minimum Practice: Conservation Practices to Reduce Nutrient Loss


Does the plan specify a 100-foot setback or a 35-foot vegetated buffer or alternative setback
for land application from downgradient surface waters and conduits in accordance with the
Effluent Limitations Guideline? .....................................................................................  N/A  Yes

 No

If an alternative setback has been specified, what is the basis for the use of an alternative
setback? __________________________________________________________
__________________________________________________________________
__________________________________________________________________


Does the plan include the use of best management practices (BMPs) to control nutrient loss from the:
Production area .......................................................................................................  N/A  Yes
Land application area(s) ..........................................................................................  N/A  Yes

 No
 No

If yes, identify:
Land Application Areas
Production Area
 Vegetated Buffers (Type of vegetation_________)
 Vegetated Buffers (Type of vegetation________)
 Diversion
 Other __________________________________
 Grassed Waterway (Type of vegetation__________)
 Strip Cropping
 Residue Management
 Terracing
 Conservation Tillage


If BMPs are being used to control nutrient loss, does the plan specify how they are to be
implemented? ............................................................................................................................  Yes

 No

If yes, what does the plan require? ______________________________________________
______________________________________________________________________

 What references are cited for the practices?  USDA Practice Standards  State Standards

 Other ______________________________ (Note: To be used to verify proper implementation)



Does the plan include Operation & Maintenance requirements for practices used to reduce
nutrient loss? .............................................................................................................................  Yes

 No



Do the plan and facility maps identify the specific locations where the BMPs and setbacks are
to be used? ..................................................................................................................  N/A  Yes

 No

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist
Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-7

H-7

NPDES Permit Writers’ Manual for CAFOs

Terms for Minimum Practice: Conservation Practices to Reduce Nutrient Loss (identify below or reference NMP
section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Minimum Practice: Protocols for Manure and Soil Testing


Does the plan include specific protocols for the representative sampling of manure, wastewater,
and soil for determining nutrient content?..................................................................................  Yes

 No



Does the plan include appropriate frequencies for the sampling of manure, wastewater, and
soil for determining nutrient content? ........................................................................................  Yes

 No



Does the plan include specific protocols for the analysis of manure, wastewater, and soil for
determining nutrient content? ....................................................................................................  Yes

 No



Are the soil test results used to develop the plan less than 5 years old? ...................................  Yes

 No

Are the manure nutrient analysis results used to develop the plan less than 12 months old? ...  Yes  No
[Note: book values may be used for the first year of operation.]
Terms for Minimum Practice: Protocols for Manure and Soil Testing (identify below or reference NMP section(s)):
_____________________________________________________________________________________________


_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Minimum Practice: Protocols for Land Application of Manure and Wastewater
Manure, Litter, and Process Wastewater Use and Disposal


What manure utilization options are identified in the plan? (If more than one option is identified in the plan,
indicate the relative amount of the manure used or disposed of under this option.)
 Land Application ............................................................................................................................... _____%
 Composting ...................................................................................................................................... _____%
 Incineration ....................................................................................................................................... _____%
Does the plan address what is done with the remaining ash? ____________________
_________________________________________________________________
 Other ................................................................................................................................................ _____%
Describe:_____________________________________________________________
_________________________________________________________________



Is manure, litter, or wastewater to be transferred off-site?

 Yes

 No

If yes:
How much will be transferred annually? __________________ tons ______________________ gallons
Does the plan include the necessary arrangements for that transfer? ..............................  Yes

 No

Does the plan identify the recipients? ..............................................................................  Yes

 No

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist

H-8

Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-8

NPDES Permit Writers’ Manual for CAFOs



If the plan includes land application of manure, litter, or process wastewater:
Do the facility maps identify the fields or conservation management units (CMU)
used to develop the plan? (Field boundaries, field number, acreage) .........................  Yes

 No

Does the plan address rates of application using the  linear approach or the  narrative rate approach?
[Note: The linear and narrative rate approaches primarily influence identification of terms
based on the NMP and generally do not dictate the content of the NMP, with a few
specific exceptions. The questions in the sections below identify specific information
that is required to support development of terms under a particular approach.]


How many acres under control of the CAFO (e.g., owned, leased, subject to an access
agreement) are identified in the plan for land application use?
_________ acres owned _________acres leased _________ total acres applied



Does the CAFO own or control sufficient land to properly use all manure and wastewater
generated by the operation?......................................................................................................  Yes

 No

If no:
Does the plan identify the quantity of excess manure being generated? ________tons/year or gallons/year
Does the plan identify how the excess manure is to be used? .............................................  Yes  No
If yes, how?___________________________________________________________
Terms for Minimum Practice: Protocols for Land Application of Manure and Wastewater, Manure, Litter, and Process
Wastewater Use and Disposal (identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Crop Production Information

For use where the NMP includes land application of manure, litter, or process wastewater


Does the plan identify what crops are produced for each field? ................................................  Yes

 No

What are they?____________________________________________________________
_________________________________________________________________


Does the plan identify the crop rotations? .................................................................................  Yes

 No

What is the crop rotation?____________________________________________________
_________________________________________________________________
Does the plan identify cropping practices? ................................................................................  Yes
If yes, what are they?


 Ridge Till
 Conservation Tillage
 Other _______________________________

 Contour Farming

Does the cropping system use irrigation? ..................................................................................  Yes
If yes, what type:
 Traveling Gun
 Center Pivot
 Flood
 Other Sprinkler
 Ridge and furrow
 Other___________________________

 For plans using the narrative rate approach, does the plan identify alternative crops for

specific fields? ..........................................................................................................................  Yes
[Note: Inclusion of alternative crops is optional.]

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist
Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

 No

 No

 No

H-9

H-9

NPDES Permit Writers’ Manual for CAFOs



Are realistic crop yield goals identified in the plan (including for alternative crops, if included
in plans using the narrative rate approach)? .............................................................................  Yes



What source of information was used to determine the realistic yield goals for this operation?
 Farm records (Circle one: last year’s crop production, 3-year average, 5- year average,
Other: __________________________________________________________________)
 USDA
 State databases (VALUES, MASCAP)
 County averages
 Previous crop insurance records

 No

 Is adequate justification provided to support the yield goal? .....................................................  Yes  No
Terms for Minimum Practice: Protocols for Land Application of Manure and Wastewater, Crop Production Information
(identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Rate Determination/Nutrient Application Information

For use where the NMP includes land application of manure, litter, or process wastewater


Does the plan clearly identify field-specific maximum application rates, as follows:
For plans using the linear approach, the maximum pounds of N and P from manure, litter,
and process wastewater per crop, per year?.............................................................................  Yes

 No

For plans using the narrative rate approach, the maximum pounds of N and P from all
nutrient sources per crop, per year? ..........................................................................................  Yes

 No



Does the plan include the outcome of a field-specific N and P transport risk assessment?....... Yes

 No



Does the plan identify the basis/rationale for determining an N-based or P-based
application rate for each field?...................................................................................................  Yes

 No

What is the basis?
 Soil test method

 Soil phosphorus threshold

 Phosphorus Index

 Other____________________________________________



Does the plan identify fields where land application is N-based and where it is P-based? ........  Yes

 No



For P-based fields, does the plan include the use of multi-year P application? .........................  Yes

 No

If yes,
Is multi-year P application limited to fields that do not have a high potential for P runoff to
surface water? .......................................................................................................................  Yes

 No

Is the application rate limited to the annual crop N requirement? ..........................................  Yes

 No

Is additional P application planned only after the amount applied in the multi-year application has been
removed through crop uptake and harvest? ..........................................................................  Yes  No


Does the plan identify the appropriate crop N and P removal rates or nutrient recommendations
(including for alternative crops, if included in plans using the narrative rate approach)? ...........  Yes



Does the plan take into account other sources of nutrients used at the operation ....................  Yes
If yes, what other sources of nutrients have been accounted for?
 Commercial fertilizer
 Biosolids
 Bedding
 Legume credits
 Wastewater
 Previous manure application
 Compost
 Irrigation water
 Other ________________________________________

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist

 No
 No

H-10

Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-10

NPDES Permit Writers’ Manual for CAFOs



For plans using the linear approach, does the plan clearly articulate the methodology used
to account for the amount of N and P in the manure to be applied?..........................................  Yes



For plans using the narrative rate approach, does the plan clearly articulate the methodology
used to account for the following? ............................................................................................  Yes
(check each that is addressed in the NMP methodology)

 No
 No

 Soil test results

 The form and source of manure

 Credits for all plant available N in the field

 The timing and method of land application

 The amount of N and P in the manure to be applied

 Volatilization of N

 Consideration of multi-year P application

 Mineralization of organic N

 Accounting for all other additions of plant available N and P to the field


Does the plan identify the application method? .........................................................................  Yes
If yes, what method is used:
 Surface applied
 Injected
 Incorporated

 No



Does the plan identify appropriate volatilization rates based on the method of application? .....  Yes

 No



Does the plan include the application of wastewater to fields via an irrigation system? ............  Yes

 No

If yes:
Does the plan identify the type of irrigation system? ..........................................................  Yes
Does the plan include provisions to minimize ponding or puddling of
wastewater on land application fields? ...............................................................................  Yes
Does the plan address the management of drainage water to prevent
surface or groundwater contamination? .............................................................................  Yes

 No

Does the plan include specific restrictions or adequate management practices to prevent water
pollution from the application of manure/wastewater to flooded, saturated, frozen, or snowcovered ground? .......................................................................................................................  Yes

 No



Does the plan address inspection and maintenance of land application equipment? ................. Yes

 No



Does the plan require periodic calibration of manure application equipment? ............................ Yes

 No



Are the application rates identified in the plan appropriate? ....................................................... Yes

 No



 No
 No

Notes: _______________________________________________________________
_______________________________________________________________
_______________________________________________________________
Terms for Minimum Practice: Protocols for Land Application of Manure and Wastewater, Rate Determination/Nutrient
Application Information (identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist
Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-11

H-11

NPDES Permit Writers’ Manual for CAFOs

Minimum Practice: Record Keeping




Identify the records that the plan indicates will be maintained at the facility.
 Production Area Records
 Weekly inspections of stormwater and runoff diversion devices and devices for
channeling contaminated stormwater to wastewater containment structures...................  Yes
 Weekly inspections of manure, litter, and process wastewater impoundments ................  Yes
 Weekly storage facility wastewater level, as indicated on a depth marker .......................  Yes
 Daily water line inspections ..............................................................................................  Yes
 Actions taken to correct deficiencies identified as a result of daily and weekly
inspections .......................................................................................................................  Yes
 Manure/wastewater storage—date of emptying, level before emptying, and level
after emptying, or quantity removed (dry manure) ...........................................................  Yes
 The date, time, and volume of any overflow .....................................................................  Yes
 Records documenting that mortalities were not disposed of in any liquid manure or
process wastewater system and that mortalities were handled to prevent the discharge
of pollutants to surface water ...........................................................................................  Yes
 On-site precipitation .........................................................................................................  Yes
 Animal Inventory ..............................................................................................................  Yes
 Land Application Records
 Manure and wastewater sample nutrient analysis test methods and results that will be
used to calculate land application rates............................................................................  Yes
 Soil sample analysis test methods and results that will be used to calculate land
application rates ...............................................................................................................  Yes
 Manure and wastewater application equipment inspection log ........................................  Yes
 Maintenance log of all equipment necessary to control discharge and meet permit
requirements (e.g., maintenance of land application equipment) ....................................  Yes
 Annual calculation of the maximum amount of manure or wastewater to be land
applied, before application ...............................................................................................  Yes
 Crop planting/harvest dates by field or CMU ....................................................................  Yes
 Crop type and yield by field or CMU – bushels/acre (seasonally) ....................................  Yes

 No
 No
 No
 No
 No
 No
 No
 No
 No
 No

 No
 No
 No
 No
 No
 No
 No

 For each land application event, the date, rate (tons of manure or gallons of
wastewater/acre or pounds of N and P per acre), weather conditions during and for
24 hours before and after application, application method, and equipment used by
field or CMU (daily during application)..............................................................................  Yes
 The total amount of N and P applied to each field, including calculations ........................  Yes
 Lease/Rental/Access Agreements for all land not owned by the operator .......................  Yes
 Off-site Transfer of Manure and Wastewater Records
 Date of each transfer ........................................................................................................  Yes
 The name and address of the recipient (for each transfer)...............................................  Yes
 Quantity transferred (for each transfer) ............................................................................  Yes
 Documentation that the most current nutrient analysis was provided to the recipient ......  Yes

 No
 No
 No
 No

Does the plan require that any additional records be maintained at the facility? .......................  Yes

 No

 No
 No
 No

If yes, what are those records? _________________________________________________
___________________________________________________________________


Does the plan include an emergency action plan to address spills and catastrophic events? ..  Yes

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist

 No

H-12

Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-12

NPDES Permit Writers’ Manual for CAFOs

Terms for Minimum Practice: Record Keeping (identify below or reference NMP section(s)):
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Part C – Determination of Plan Adequacy
[Note: This section is to be used by the NMP reviewer to evaluate the overall adequacy of the plan based on the
information in Parts A and B and does not necessarily reflect information expected to be contained in the NMP.]


Does the plan adequately address the storage, handling, and application of manure and
wastewater to prevent the discharge of pollutants to waters of the United States? ...................  Yes

 No



Is the plan consistent with the technical standards for nutrient management established by
the Director with regard to protocols for manure and soil testing and land application protocols
including nutrient transport risk assessment methods and methods and data used to determine
application rates? ......................................................................................................................  Yes

 No

Have there been past discharges to waters of the United States from the facility? ...................  Yes

 No

If yes, does the plan include sufficient measures to address the cause of the past discharge
and prevent future discharges? ...................................................................................  Yes

 No

Does the plan require revision? .................................................................................................  Yes

 No





If yes, what specific components of the plan require revision?
_________________________________________________________________________________
_________________________________________________________________________________
_________________________________________________________________________________
_________________________________________________________________________________
_________________________________________________________________________________
_________________________________________________________________________________
_________________________________________________________________________________
_________________________________________________________________________________
_______________________________________________________________

Additional Review Comments:

_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________
_____________________________________________________________________________________________

Appendix H. NPDES CAFO Nutrient Management Plan Review Checklist
Appendix H: NPDES CAFO Nutrient Management Plan Review Checklist

H-13

NPDES Permit Writers’ Manual for CAFOs

Appendix

I

NPDES CAFO Technical
Standard Review
Checklist
Under the Clean Water Act, all authorized states were required to adopt technical standards
by February 12, 2005, pursuant to Title 40 of the Code of Federal Regulations (CFR) part 123.36.
Part 123.36 requires that technical standards meet the requirements of 40 CFR part 412.4(c)
(2) to minimize phosphorus (P) and nitrogen (N) transport to surface waters. Additionally,
the 2008 confined animal feeding operation (CAFO) rule requires site-specific terms of a
nutrient management plan (NMP) to be included in a CAFO’s National Pollutant Discharge
Elimination System (NPDES) permit. Technical standards provide the basis for critical
elements of the site-specific terms of the NMP required by 40 CFR parts 122.42(e)(5)(i) and (ii).
The criteria outlined in the attached checklist identifies the information needed in a technical
standard to meet the requirements ofpart 412.4(c)(2) to develop an NMP that contains all the
required terms of the NMP.

NPDES Permit Writers’ Manual for CAFOs

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NPDES Permit Writers’ Manual for CAFOs

ESTABLISHMENT AND APPLICABILITY OF TECHNICAL STANDARDS (TS)
1

Has the Director verified or provided (or
both) the state’s TS?

2

What mechanism did the state Director
use to establish the TS?

Standalone document

(check item(s) to right)

Permit referenced documents

Permit attachment
Written into the regulations
Regulation reference documents
Other

3

How is the specific standard included as a Describe how it is made known that the CAFO NMP must be developed in
requirement of the CAFO program?
accordance with the document(s) identified above. For example, does the permit
or regulation provide a reference to the listed document(s)? Or does the document
itself identify that it is the TS for CAFO operations that meets the requirement of
part 412.4(c)(2)?

APPLICATION RATES
Field-specific risk assessment
Specify

Reference

4

Does the TS contain a clearly outlined,
field-specific assessment tool for N or P
or both transport from the field to surface
waters?

Criteria

Answer Y or N; Describe
what the assessment tool is

Provide a reference to where in the TS this is stated

5

Does the assessment tool (above)
provide quantitative or qualitative (or
both) criteria for determining whether
manure application rates can be N-based,
P-based, or prohibited?

Answer Y or N; Provide the Provide a reference to where in the TS this is stated
quantitative criteria and
corresponding rate (e.g.,
1.5xP removal, 2xP removal,
3xP removal)

6

Where the assessment tool requires a
Answer Y or N; If no, provide Provide a reference to where in the TS this is stated
P-based application rate, is it constrained under what criteria this is
to a 1-year P removal rate?
allowed and what rate is
allowed

Amount
Criteria

Specify

Reference
Provide a reference to where in the TS this is stated

7

Does the TS provide the basis for
determining expected crop yields?

Answer Y or N; Explain how
realistic yield goals are to
be calculated or determined
and provide any necessary
sources of information that
are to be used.

8

Does the TS provide crop
recommendations that are to be used on
which to base applications rates?

Answer Y or N; Provide the Provide a reference to where in the TS this is stated
recommendations that are to
be used for different crops
and their source

9

Does the TS define what a P-based
application rate is? (e.g., crop removal
rate, soil test, or the choice of either)?

Answer Y or N; Provide
what it is

10

Does the TS provide the actual removal
rates, soil test recommendations or both
for crops, depending on the answer to
item 9?

Answer Y or N; Provide what Provide a reference to where in the TS this is stated
the removal rate is or the
soil test recommendation

Provide a reference to where in the TS this is stated

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Amount (continued)
Criteria

Specify

Reference

11

Does the TS provide a value for N credits
to be given when legume crops are
planted?

Answer Y or N; Provide what Provide a reference to where in the TS this is stated
N credits are applied for
different legumes

12

Are N mineralization rates provided for
different type (dairy, beef, poultry, swine,
etc.) of manure?

Answer Y or N; Provide
rates with corresponding
manure types

Provide a reference to where in the TS this is stated

13

Does the TS address the requirement for
a manure1 analysis?

Answer Y or N

Provide a reference to where in the TS this is stated

14

Does the TS address the frequency of a
manure† analysis

Answer Y or N; Provide
frequency for analysis to be
performed

Provide a reference to where in the TS this is stated

15

Does the TS address methods for
collecting manure† samples?

Answer Y or N; Provide
methods to be used

Provide a reference to where in the TS this is stated

16

Does the TS address the components for
which the manure† is to be analyzed?

Answer Y or N; List
components to be analyzed

Provide a reference to where in the TS this is stated

17

Does the TS address acceptable
method(s) or laboratories or both for
conducting the manure† analysis?

Answer Y or N; Provide
methods or appropriate
laboratories to be used

Provide a reference to where in the TS this is stated

18

Does the TS address the requirement for
a soil test?

Answer Y or N

Provide a reference to where in the TS this is stated

19

Do the TS address the frequency of the
soil test?

Answer Y or N; Provide
frequency for analysis to be
performed

Provide a reference to where in the TS this is stated

20

Does the TS address the methods for
collecting soil samples?

Answer Y or N; Provide
methods to be used

Provide a reference to where in the TS this is stated

21

Does the TS address which components
to include in the soil analysis?

Answer Y or N; List
components to be analyzed

Provide a reference to where in the TS this is stated

22

Does the TS address acceptable
method(s) or laboratories or both for
conducting the soil analysis?

Answer Y or N; Provide
methods or laboratories to
be used

Provide a reference to where in the TS this is stated

Form and Source
Criteria
23

Does the amount, timing, and method
address how it is to be applied to each
form (solid, semisolid, or liquid) and
source of manure?

Specify

Reference

The form and source of manure can be addressed separately under the amount,
timing, or method of land application as it applies.

Timing—The criteria below are not required to adequately address the timing of manure application. The criteria identified
below may be addressed in a TS, although alternative criteria that address the timing of manure application would also be
appropriate.
Criteria

Specify

24

Does the TS address when manure
Answer Y or N; If yes,
application should be prohibited or
provide when it is to be
delayed? If yes, do these limitations apply delayed
only to certain forms (solid, semisolid, or
liquid) of manure?

25

Does the TS adjust mineralization rates
for applications made at different times
during the year?

Appendix I. NPDES CAFO Technical Standard Review Checklist

Reference
Provide a reference to where in the TS this is stated

Answer Y or N; Provide rate Provide a reference to where in the TS this is stated
to be used for different times
of land application

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Method of Application—The criteria below are not required to adequately address the method of manure application. The
criteria identified below may be addressed in a TS, although alternative criteria that address the method of manure application
would also be appropriate.
Criteria

Specify

Reference

26

Does the TS provide volatilization rates to Answer Y or N; Provide rate
apply to different types of land application and corresponding landmethods? (e.g., if manure is incorporated application method
after X number of days, a different
volatilization rate is applied)?

Provide a reference to where in the TS this is stated

27

Are there any specifications provided for
applying different forms (solid, semisolid,
or liquid) of manure?

Answer Y or N; Provide any
specifications that must be
met when land applying
different forms of manure
(e.g., application of liquid
waste through surface
or sprinkler irrigation will
be timed to prevent deep
percolation or runoff. The
application rate must not
exceed the soil intake/
infiltration rate.)

Provide a reference to where in the TS this is stated

Specify

Reference

Appropriate Flexibilities
Criteria

1

28

Does the TS allow multi-year P
application?

Answer Y or N; If yes, define Provide a reference to where in the TS this is
what multi-year application stated. This flexibility does not have to be provided
means for this standard
for by the state Director. If it is not provided for, the
remaining criteria (29 – 31) are not applicable.

29

If yes, does it provide restrictions on when Answer Y or N; provide
or where (or both) this can occur?
restrictions that apply

Provide a reference to where in the TS this is stated

30

If yes, is there a restriction that additional
P to these fields may not be applied until
the amount applied in the single year has
been removed through plant uptake and
harvest?

Answer Y or N

Provide a reference to where in the TS this is stated

31

If yes, does the standard set N limits that
must be met?

Answer Y or N; Provide N
limits that must be met

Provide a reference to where in the TS this is stated

Manure in this checklist means manure, litter, or process wastewater.

Appendix I. NPDES CAFO Technical Standard Review Checklist

NPDES Permit Writers’ Manual for CAFOs

Appendix
NPDES General Permit
Template for CAFOs

J

NPDES Permit Writers’ Manual for CAFOs

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NPDES Permit Writers’ Manual for CAFOs

NOTE: This NPDES General Permit template for CAFOs has been developed to address existing large
CAFOs subject to the effluent limitation guidelines subparts C (dairy cows and cattle other than veal
calves) and D (swine, poultry, and veal calves). This example permit has not been developed for new
sources or for CAFOs subject to subparts A (horses and sheep) and B (ducks).
Example NPDES CAFO Permit Text Key:
[BOLD/SMALL CAPITALS] defines areas where the permitting authority needs to insert specific text.
[Bold/Italic] provides notes to the permitting authority designed to help it develop an NPDES CAFO
permit and should be deleted when using this template.

TEMPLATE
NPDES GENERAL PERMIT
FOR
CONCENTRATED ANIMAL FEEDING OPERATIONS (CAFOs)
[Authorized NPDES Permitting Authority]
AUTHORIZATION TO DISCHARGE UNDER THE
NATIONAL POLLUTANT DISCHARGE ELIMINATION SYSTEM (NPDES)
[The intent of this NPDES General Permit template for CAFOs is to provide an outline for specific
permit requirements that are consistent with the NPDES CAFO regulations, CAFO ELG, and the
NPDES CAFO Permit Writers’ Guidance (to be updated in accordance with the 2008 final rule).
EPA encourages permitting authorities to use the recommendations of the guidance manual and
this template as appropriate. Minimum NPDES permitting requirements for CAFOs are defined at
40 CFR parts 122, 123, and 412 and all other applicable CWA regulations.]
In compliance with provisions of the Clean Water Act, 33 United States Code (U.S.C.) 1251 et seq. (the
Act), [Insert State Regulatory Citation as Appropriate], owners and operators of concentrated
animal feeding operations (CAFOs), except those CAFOs excluded from coverage in Part I of this
permit, are authorized to discharge and must operate their facility in accordance with effluent
limitations, monitoring requirements, and other provisions set forth herein.
A copy of this permit must be kept by the permittee at the site of the permitted activity.
This permit will become effective [Date 30 Days After: Date of Publication (General permit) or
Signature (Individual Permit)]
This permit and the authorization to discharge under the NPDES shall expire at midnight [Date 5
Years After the Date Above].
Signed this [Day] of [Month] and [Year] .
[Permitting Authority—Official]

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Contents
Part I.

Permit Area and Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-3
A. Permit Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-3
B. Permit Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-3
C. Eligibility for Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-3
D. Limitations on Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-4
E. Application for Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-4
F. Requiring an Individual Permit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-6
G. Permit Expiration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-6
H. Change in Ownership . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-7
I. Termination of Permit Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-7

Part II.

Effluent Limitations and Standards and Other Legal Requirements . . . . . . . . . . . . . . . J-8
A. Effluent Limitations and Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-8
B. Other Legal Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-14

Part III. Effluent Limitations and Standards of the Nutrient Management Plan . . . . . . . . . . . . . J-14
A. Procedural Requirements for Implementing the Terms of the Nutrient
Management Plan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-14
B. Terms of The Nutrient Management Plan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-22
Part IV. Special Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-23
A. Facility Closure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-23
B. Additional Special Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-24
Part V.

Discharge Monitoring and Notification Requirements . . . . . . . . . . . . . . . . . . . . . . . J-24
A. Notification of Discharges Resulting from Manure, Litter, and Process
Wastewater Storage, Handling, On-site Transport and Application . . . . . . . . . . . . . . J-24
B. Monitoring Requirements for All Discharges from
Retention Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-24
C. General Inspection, Monitoring, and Record-Keeping Requirements . . . . . . . . . . . . . J-25
D. Additional Monitoring Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-28

Part VI. Annual Reporting Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-28
Part VII. Standard Permit Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-29
A. General Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-29
B. Proper Operation and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-32
C. Monitoring and Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-33
D. Reporting Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-33
E. Signatory Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-35
F. Certification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-36
G. Availability of Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-36
H. Penalties for Violations of Permit Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-36
Part VIII. Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-37
Appendix A. (Insert Form 2B/Notice of Intent or Appropriate State Form) . . . . . . . . . . . . . . . . J-40
Appendix B. (Insert State Technical Standards for Nutrient Management) . . . . . . . . . . . . . . . . J-40
Appendix C. Historic Properties Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-40
Appendix D. Notice of Termination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . J-40

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Part I. Permit Area and Coverage
A. Permit Area
[The permitting authority should insert language that identifies the scope of the permit. In the
case of a general permit, the permit should identify the type of facilities and/or the geographic
area covered (e.g., watershed, statewide) by the permit. If the general permit is restricted to
specific animal types and/or to certain size facilities, those limitations should be identified
here. When issuing individual permits, this section of the permit should identify the specific
facility covered by the permit. Only facilities that discharge or propose to discharge are
required to apply for an NPDES permit. Other CAFOs may seek permit coverage if desired.]

B. Permit Coverage
This permit covers any operation that meets the following criteria:
1. Is located in the permit area as defined by Part I.A. of this permit.
2. That meets the definition of a CAFO at 40 CFR part 122.23(b)(4) (see Part VIII,
Definitions, large CAFO of this permit) [Insert State Regulatory Citation as
Appropriate].
3. Discharges pollutants to waters of the United States. Once an operation is defined
as a CAFO, the NPDES requirements for CAFOs apply with respect to all animals in
confinement at the operation and all manure, litter and process wastewater generated
by those animals or the production of those animals, regardless of the type of animal.
4. Is eligible for permit coverage as defined in Part I.C .of this permit.
5. Is authorized for permit coverage by the permitting authority as specified in Part I.F. of
this permit.

C. Eligibility for Coverage
Unless excluded from coverage in accordance with Paragraph D or F below, owners/operators of
existing, operating animal feeding operations that are defined as CAFOs or designated as CAFOs
by the permitting authority (see Part VIII Definitions, CAFOs of this permit) and that are subject
to 40 CFR Part 412, subparts C (Dairy Cows and Cattle Other than Veal Calves) and D (Swine,
Poultry, and Veal Calves) are eligible for coverage under this permit. Eligible CAFOs may apply
for authorization, under the terms and conditions of this permit, by submitting a Notice of Intent
(NOI) to be covered by this permit (see Appendix A of this permit). [The permitting authority
should provide a copy of the NOI as an appendix to this permit.]
CAFO owners/operators may also seek to be excluded from coverage under this permit by
(1) submitting to the permitting authority a Notice of Termination form (see Appendix D of this

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permit). [The permitting authority should specify the information to be included in such a
request or, if available, the form to be used and include a copy of the form as an appendix to
the permit.] or (2) by applying for an individual NPDES Permit in accordance with Part I.F of this
permit.
[The permitting authority should specify an overall approach that defines how CAFOs are to be
permitted. That requires determining those types of CAFOs that will be addressed under either
general (statewide or watershed) or individual permits. The approach should be modified, as
necessary, to reflect specific permitting authority programmatic priorities and constraints.]

D. Limitations on Coverage
The following CAFOs are not eligible for coverage under this NPDES general permit and must
apply for an individual permit: [Specific eligibility limitations for the general permit should be
determined by the NPDES permitting authority.]

E. Application for Coverage
[The permitting authority should insert the appropriate text in this section. Two alternatives
are provided for E.1 providing different levels of detail.]
1. Owners/operators of CAFOs seeking to be covered by this permit must perform the
following:
a. For facilities covered by an expiring or expired permit that wish to have continuous
permit coverage, submit an NOI to the permitting authority within [The permitting
authority may establish a time frame for submitting the NOI, which may extend
to the expiration date of the permit or some time before the expiration date.]
days of the effective date of this permit.
b. Submit a Nutrient Management Plan (NMP) with the NOI that meets the
requirements of 40 CFR Parts 122 and 412, where applicable.
c. Submit an NOI after the applicable date in Part I. E.1.a. above. Regardless of when
the NOI is submitted, the CAFO’s authorization under this permit is only for
discharges that occur after permit coverage is granted. The permitting authority
reserves the right to take appropriate enforcement actions for any unpermitted
discharges.

[Where a CAFO has submitted an application for coverage under an individual
permit before issuance of the general permit, the CAFO must (1) submit an NOI
for coverage under the general permit, or (2) submit an updated application for
coverage under an individual permit if the application requirements have been
revised or if the information in the existing application is not current.]

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2. Contents of the NOI: The NOI submitted for coverage under this permit must include
the following information:
a. Name of the owner or operator.
b. Facility location and mailing addresses.
c. Latitude and longitude of the production area (entrance to production area).
d. Topographic map of the geographic area in which the CAFO is located showing the
specific locations of the production area, land application area, and the name and
location of the nearest surface waters.
e. A diagram of the production area.
f. Number and type of animals, whether in open confinement or housed under roof
(beef cattle, broilers, layers, swine weighing 55 pounds or more, swine weighing
less than 55 pounds, mature dairy cows, dairy heifers, veal calves, sheep and
lambs, horses, ducks, turkeys, other).
g. Type of containment and storage (anaerobic lagoon, roofed storage shed, storage
ponds, underfloor pits, aboveground storage tanks, belowground storage tanks,
concrete pad, impervious soil pad, other) and total capacity for manure, litter, and
process wastewater storage (tons/gallons). [Note: Total design storage volume
includes all wastes accumulated during the storage period, and as applicable;
normal precipitation less evaporation on the surface of the structure during the
storage period; normal runoff from the production area for the storage period;
the direct precipitation from a 25-year, 24-hour storm on the surface of the
structure; the runoff from the 25-year, 24-hour storm from the production area;
residual solids; and necessary freeboard to maintain structural integrity.]
h. Total number of acres under control of the applicant available for land application
of manure, litter, or process wastewater.
i. Estimated amounts of manure, litter, and process wastewater generated per year
(tons/gallons).
j. Estimated amounts of manure, litter and process wastewater transferred to other
persons per year (tons/gallons).
k. An NMP that meets the requirements of the provisions of 40 CFR part 122.42(e)
(including, for all CAFOs subject to 40 CFR part 412, subpart C or subpart D, the
requirements of 40 CFR part 412.4(c), as applicable) and Part III of this permit.
3. Signature Requirements: The NOI must be signed by the owner/operator or other
authorized person in accordance with Part VII.E of this permit.
4. Where to Submit: Signed copies of the NOI or individual permit application must be
sent to: [Permitting Authority Mailing Address].

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5. Upon receipt, the permitting authority will review the NOI and NMP to ensure that
the NOI and NMP are complete. The permitting authority may request additional
information from the CAFO owner or operator if additional information is necessary to
complete the NOI and NMP or to clarify, modify, or supplement previously submitted
material. If the permitting authority makes a preliminary determination that the NOI
is complete, the NOI, NMP and draft terms for the NMP to be incorporated into the
permit will be made available for a thirty (30) day public review and comment period.
The process for submitting public comments and requests of hearing will follow the
procedures applicable to draft permits as specified by 40 CFR parts 124.11 through
124.13. The permitting authority will respond to comments received during the
comment period as specified in 40 CFR part 124.17 and, if necessary, require the CAFO
owner or operator to revise the NMP in order to granted permit coverage. If determined
appropriate by the permitting authority, CAFOs will be granted coverage under this
general permit upon written notification by EPA. The permitting authority will identify
the terms of the NMP to be incorporated into the permit in the written notification.

F. Requiring an Individual Permit
1. The [PERMITTING AUTHORITY], may at any time require any facility authorized
by this permit to apply for and obtain an individual NPDES permit. [PERMITTING
AUTHORITY] will notify the operator, in writing, that an application for
an individual permit is required within [TIME FRAME FOR APPLICATION
SUBMISSION]. Coverage of the facility under this general NPDES permit is
automatically terminated when (1) the operator fails to submit the required
individual NPDES permit application within the defined time frame or (2) the
individual NPDES permit is issued by [PERMITTING AUTHORITY].
2. Any owner/operator covered under this permit may request to be excluded from the
coverage of this permit by applying for an individual permit. The owner/operator shall
submit an application for an individual permit (Form 1 and Form 2B) with the reasons
supporting the application to the [Permitting Authority]. If a final, individual
NPDES permit is issued to an owner/operator otherwise subject to this general permit,
the applicability of this NPDES CAFO general permit to the facility is automatically
terminated on the effective date of the individual NPDES permit. Otherwise, the
applicability of this general permit to the facility remains in full force and effect (for
example, if an individual NPDES permit is denied to an owner/operator otherwise
subject to this general permit).

G. Permit Expiration
This permit will expire 5 years from the effective date. The permittee must reapply for permit
coverage 180 days before the expiration of this permit unless the permit has been terminated
consistent with 40 CFR part 122.64(b) or the CAFO will not discharge or propose to discharge upon
expiration of the permit. If this permit is not reissued or replaced before the expiration date, it will

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be administratively continued in accordance with the Administrative Procedures Act and remain
in force and effect. Any permittee who is granted permit coverage before the expiration date will
automatically remain covered by the continued permit until the earlier of any of the following:
1. Reissuance or replacement of this permit, at which time the permittee must comply
with the NOI conditions of the new permit to maintain authorization to discharge.
2. Issuance of an individual permit for the permittee’s discharges.
3. A formal decision by the permitting authority not to reissue this general permit, at
which time the permittee must seek coverage under an individual permit.
4. The permitting authority grants the permittee’s request for termination of permit
coverage.

H. Change in Ownership
If a change in the ownership of a facility whose discharge is authorized under this permit occurs,
coverage under the permit will automatically transfer if (1) the current permittee notifies the
permitting authority at least 30 days prior to the proposed transfer date; (2) the notice includes a
written agreement between the existing and new permittees containing a specific transfer date
for permit responsibility, coverage, and liability; and (3) the permitting authority does not notify
the existing permittee and the proposed new permittee of its intent to modify or revoke and
reissue the permit. If the new CAFO owner or operator modifies any part of the NMP, the NMP
shall be submitted to the permitting authority in accordance with Part III.A of this permit and
40 CFR part 122.42(e)(6).

I. Termination of Permit Coverage
1. Coverage under this permit may be terminated in accordance with 40 CFR part 122.64
and if EPA determines in writing that one of the following three conditions are met:
a. The facility has ceased all operations and all wastewater or manure storage
structures have been properly closed in accordance with [The appropriate
standard for closure for example, Natural Resource Conservation Service
(NRCS) Conservation Practice Standard No. 360, Closure of Waste
Impoundments, as contained in the Natural Resources Conservation Service
Field Office Technical Guide] and all other remaining stockpiles of manure, litter,
or process wastewater not contained in a wastewater or manure storage structure
are properly disposed.
b. The facility is no longer a CAFO that discharges manure, litter, or process
wastewater to waters of the United States.
c. In accordance with 40 CFR part 122.64, the entire discharge is permanently
terminated by elimination of the flow or by connection to a publicly owned
treatment works (POTW).

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Part II. Effluent Limitations and Standards and Other
Legal Requirements
A. Effluent Limitations and Standards
[The permit writer will include (1) technology-based effluent limitations, and (2) any more
stringent water quality-based effluent limitations where necessary to prevent discharges
from the production area that would cause or contribute to an exceedance of water quality
standards.]
The following effluent limitations apply to facilities covered under this permit:
[These provisions apply to all existing facilities that are subject to the CAFO ELG specified in
40 CFR part 412 parts C and D. In other cases, the permit writer establishes technology-based
limitations on the basis of the specific requirements defined in the CAFO ELG or through the
application of best professional judgment (BPJ), whichever is determined to be applicable.]
1. Technology-based Effluent Limitations and Standards—Production Area.
The CAFO must implement the terms of an NMP, as specified below and in Part III.B of
this permit.
a. There may be no discharge of manure, litter, or process wastewater pollutants into
waters of the United States from the production area except as provided below:

Whenever precipitation causes an overflow of manure, litter, or process wastewater,
pollutants in the overflow may be discharged into waters of the United States provided:
i. The production area is properly designed, constructed, operated and maintained
to contain all manure, litter, process wastewater and the runoff and direct
precipitation from the 25-year, 24-hour storm event for the location of the CAFO.
ii. The design storage volume is adequate to contain all manure, litter, and process
wastewater accumulated during the storage period including, at a minimum, the
following:
a) The volume of manure, litter, process wastewater, and other wastes
accumulated during the storage period.
b) Normal precipitation less evaporation during the storage period.
c) Normal runoff during the storage period.
d) The direct precipitation from the 25-year, 24-hour storm.
e) The runoff from the 25-year, 24-hour storm event from the production area.
f) Residuals solids after liquid has been removed.
g) Necessary freeboard to maintain structural integrity.
h) A minimum treatment volume, in the case of treatment lagoons.

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b. Installation of a depth marker in all open surface liquid impoundments. The depth
marker must clearly indicate the minimum capacity necessary to contain the
runoff and direct precipitation of the 25-year, 24-hour rainfall event. The marker
shall be visible from the top of the levee.
c. Weekly visual inspections of all stormwater diversion devices, runoff diversion
structures, and devices channeling contaminated stormwater to the wastewater
and manure storage and containment structures.
d. Weekly inspections of the manure, litter, and process wastewater impoundments
noting the level as indicated by the depth marker installed in accordance with Part
II.A.1.b of this permit.
e. Daily visual inspections of all water lines, including drinking water and cooling
water lines.
f. Timely correction of any deficiencies that are identified in daily and weekly
inspections.
g. Proper disposal of dead animals [may specify a timeframe for example, within
3 days] unless otherwise provided for by the permitting authority. Mortalities must
not be disposed of in any liquid manure or process wastewater system that is not
specifically designed to treat animal mortalities. Animals shall be disposed of in
a manner to prevent contamination of waters of the United States or creation of a
public health hazard.
h. The maintenance of complete, on-site records documenting implementation of
all required additional measures for a period of 5 years, including the records
specified for Operation and Maintenance in Part V.C, Table V-A of this permit.
i. The production area must be operated in accordance with the additional measures
and records specific in Part II.A.2 of this permit.
2. Additional Measures–Applicable to the Production Area.
In addition to meeting the requirements in Part II.B of this permit, the permittee must
implement the following additional measures:
a. Ensure adequate storage of manure, litter, and process wastewater, including
procedures to ensure proper operation and maintenance of the storage facilities.
b. Mortality handling practices shall be in accordance with all applicable state
and local regulatory requirements. Any such state/local requirements should be
consistent with NRCS Practice Standard 316 as applicable.
c. Ensure that clean water is diverted, as appropriate, from the production area in
accordance with Part III.A.3.c of this permit.
d. Prevent direct contact of confined animals with waters of the United States.

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e. Ensure that chemicals and other contaminants handled on-site are not
disposed of in any manure, litter, process wastewater, or storm water storage or
treatment system unless specifically designed to treat such chemicals and other
contaminants.
f. Identify specific records that will be maintained to document the implementation
and management of Part II.A.2. a through c of this permit.
g. In cases where CAFO-generated manure, litter, or process wastewater is sold or
given away, the permittee must comply with the following conditions:
i. Maintain records showing the date and amount of manure, litter, and/or process
wastewater that leaves the permitted operation.
ii. Record the name and address of the recipient.
iii. Provide the recipient(s) with representative information on the nutrient content
of the manure, litter, and/or process wastewater.
iv. The records must be retained on-site, for a period of 5 years, and be submitted to
the permitting authority on request.
3. Water Quality-based Effluent Limitations and Standards—Production Area.

[Permitting authority to specify applicable water quality-based effluent
limitations.] [The permit writer must ensure that the permit includes effluent
limitations developed from applicable technology-based requirements and any
more stringent effluent limitations necessary to meet water quality standards.
A water quality-based effluent limitation is designed to protect the quality of
the receiving water by ensuring state or tribal water quality standards are met.
Federal regulations, 40 CFR part 122.44(d), require permit limitations to control
all pollutants that may be discharged at a level that will cause, have the reasonable
potential to cause, or contribute to an excursion above any state water quality
standard. Where water-quality based effluent limitations apply (i.e., are more
stringent), technology-based effluent limitations do not apply.

The permit writer determines the need to establish more restrictive requirements
for the production area, particularly for instances where the discharge is to 303(d)
waterbodies listed for nutrients, dissolved oxygen, or bacteria, or where an analysis
of frequency, duration and magnitude of the anticipated discharge (consisting
of potential overflows of manure, litter, or process wastewater) indicates the
reasonable potential to violate applicable water quality standards. With respect
to the production area, the imposition of a more restrictive water quality-based
effluent limitation can include the establishment of more restrictive requirements,
such as the imposition of a higher design standard (e.g., 100 year, 24-hour storm in
the case of existing sources under subpart C and D of the CAFO ELG) or the inclusion
of additional management practices.]

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4. Technology-based Effluent Limitations and Standard—Land Application Areas
under the Control of the CAFO Owner/Operator.

Permittees that apply manure, litter, or process wastewater to land under the
permitted CAFO’s ownership or operational control must implement the terms of an
NMP, as specified below and in Part III.B of this permit. The NMP must be developed
in accordance with the requirements of this section and Part III.A of this permit.
a. Determination of application rates. Application rates for manure, litter, or
process wastewater must minimize phosphorus and nitrogen transport from the
field to surface waters in compliance with the technical standards for nutrient
management established by the permitting authority. [Insert or Reference
Technical Standards for Nutrient Management established by the
Permitting Authority in Accordance with 40 CFR 123.36. The Technical
standard must (1) specify the field-specific assessment of the potential
for nitrogen and phosphorus transport form the field to surface
waters, (2) address the form, source, amount, timing, and method of
application of nutrients on each field to achieve realistic production
goals, and (3) include appropriate flexibilities for the implementation
of specific nutrient management practices to comply with the
standard.] [It is recommended that a complete copy of the standard established
by the permitting authority be included as an appendix to the permit.]
b. Manure and soil sampling. Manure must be analyzed at least once annually
for nitrogen and phosphorus content. Soil must be analyzed at least once every
5 years [or replace with more stringent state-specific soil sampling frequencies
for phosphorus and nitrogen]. The results of the analyses must be used in
determining application rates for manure, litter, and process wastewater.
c. Inspection of land application equipment for leaks. Equipment used for land applica­
tion of manure, litter, or process wastewater must be inspected periodically for leaks.
d. Land application setback requirements. Manure, litter, or process wastewater
must not be applied closer than 100 feet to any downgradient waters of the United
States, open tile line intake structures, sinkholes, agricultural well heads, or other
conduits to waters of the United States. The permittee may elect to use a 35-foot
vegetated buffer where applications of manure, litter, or process wastewater are
prohibited as an alternative to the 100-foot setback to meet the requirement.
e. Record Keeping requirements. Complete, on-site records including the site-specific
NMP must be maintained to document implementation of all required land
application practices. Such documentation must include the records specified for
Soil and Manure/Wastewater Nutrient Analyses and Land Application in Part V.C,
Table V-A of this permit.

[Site-specific conservation practices (other than the setback requirements in
40 CFR part 412.4(c)(5) which apply to all Large CAFOs) and protocols to land

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apply manure, litter and process wastewater are site-specific and must be
included in Part IV of this permit.]
5. Additional Measures–Applicable to the Land Application under the Control of the
CAFO Owner/Operator.

[Permitting authorities should consider the applicability of the following types of
additional limitations for land application under the control of the CAFO. Options
are not limited to the examples presented below.]
a. Additional BMPs to control discharges from land application areas. [Insert BMPs
to control discharges from land application areas, such as limiting discharges
from tile drains, areas where there is significant soil erosion, and/or runoff
associated with irrigation.]
b. Prohibitions.
i. There shall be no discharge of manure, litter, or process wastewater to waters of
the United States from a CAFO as a result of the application of manure, litter or
process wastewater to land areas under the control of the CAFO, except where
it is an agricultural stormwater discharge. Where manure, litter, or process
wastewater has been applied in accordance with the terms of the NMP as set
forth in Part II.A and III.B of this permit, a precipitation related discharge of
manure, litter, or process wastewater from land areas under the control of the
CAFO is considered to be an agricultural stormwater discharge.
ii. [Any state-specific prohibition or other limitations such as timing of land
application, (e.g., no application on frozen or snow-covered land), minimum
storage capacity, or specific BMPs required (e.g., stockpiles, prevention of the
direct contact of animals with waters of the United States).]

6. Water Quality-based Effluent Limitations and Standards–Applicable to the Land
Application under the Control of the CAFO Owner/Operator.

[Permitting authority to specify other/alternate applicable water
quality-based effluent limitations.] [Discharges from CAFOs that are not
exempt from CWA permitting requirements (i.e., agricultural stormwater discharges) are
subject to NPDES requirements, including water quality-based effluent limitations. The
permit writer may determine the need to establish effluent limitations necessary to meet
water quality standards. A water quality-based effluent limitation is designed to protect
the quality of the receiving water by ensuring state or tribal water quality standards are
met. Federal regulations, 40 CFR part 122.44(d) require permit limitations to control
all pollutants that may be discharged at a level that will cause, have the reasonable
potential to cause, or contribute to an excursion above any state water quality standard.
Water quality-based effluent limitations might be needed when there is a dry-weather
discharge (e.g., from tile drain systems or clean water irrigation on fields where manure
was previously applied) from the land application area that causes or contributes to an
excursion above any state water quality standard.]

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7. Effluent Limitations—Other Discharges.

[All discharges other than agricultural stormwater should be addressed under
a CAFO permit. Therefore, if there are situations or conditions that result in a
discharge during the term of the permit and that are not addressed under the
effluent limitations above, such discharges should be addressed either here or
in part IV.B of this permit (Special Conditions, Additional Special Conditions)
through the application of BPJ and, to the extent necessary, the use of water qualitybased effluent limitations. The language provided below includes examples. Such
conditions should be developed using state-specific requirements and CAFOspecific conditions.]
a. Process wastewater discharges from outside the production area, including:
washdown of equipment that has been in contact with manure, raw materials,
products or by-products that occurs outside the production area; runoff of
pollutants from raw materials, products or by-products (such as manure, litter,
bedding and feed) from the CAFO that have been spilled or otherwise deposited
outside the production area which are discharged to waters of the United States;
and [Insert any other discharges meeting this description] shall be
identified in the NMP. The NMP shall identify measures necessary to meet
applicable water quality standards. [Specify additional requirements here
or cross-reference requirements elsewhere in this permit]
b. Wastewater discharges that do not meet the definition of process wastewater,
including: (1) discharges associated with feed, fuel, chemical, or oil spills, equip­
ment repair, and equipment cleaning, where the equipment has not been in contact
with manure, raw materials, products or by-products; (2) domestic wastewater
discharges; and [Insert any other discharges meeting this description]
shall be identified in the NMP. The NMP shall identify measures necessary to meet
applicable water quality standards. [Specify additional requirements here or
cross-reference requirements elsewhere in this permit].
c. Stormwater discharges that are not addressed under the effluent limitations in
Section II above remain subject to applicable industrial or construction stormwater
discharge requirements. [Permit writers might want to clarify that such
stormwater excludes process wastewater, discharges that qualify as agricultural
stormwater, and discharges from construction activities that disturb less than
one acre. Permit writers also may want to discuss the applicability of the no
exposure provisions specified in 40 CFR part 122.26(g), as well as either specify
or reference the applicable stormwater requirements or reference an applicable
stormwater permit.] [Where appropriate, reference general permit or
other applicable stormwater requirements.

In addition to meeting the above effluent limitations in Part II.A of this permit, the
permittee must comply with the special conditions established in Part IV of this permit.

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B. Other Legal Requirements
No condition of this permit shall release the permittee from any responsibility or requirements
under other statutes or regulations, federal, state/Indian tribe or local.

Part III. Effluent Limitations and Standards of the
Nutrient Management Plan
A. Procedural Requirements for Implementing the Terms of
the Nutrient Management Plan
CAFO owners or operators seeking coverage under this general permit must submit a Nutrient
Management Plan (NMP) with the NOI, as required by Part I.E.1 of this permit. The NMP shall
specifically identify and describe practices that will be implemented to assure compliance with
the effluent limitations and other conditions of this permit set forth in this part and Part II.A of
this permit (Effluent Limitations and Standards). The NMP must be developed in accordance
with the technical standards identified in Appendix B of this permit. [Alternatively, technical
standards may be identified in this section.]
1. Schedule. The completed NMP must be submitted to the permitting authority with
the NOI for CAFOs seeking coverage under this permit. The CAFO shall implement its
NMP upon authorization under this permit, in accordance with the terms of the NMP
set forth in Part III.B of this permit.
2. NMP Review and Terms
a. Upon receipt of the NMP, the permitting authority will review the NMP. The
permitting authority may request additional information from the CAFO owner or
operator if additional information is necessary to complete the NMP, or to clarify,
modify, or supplement previously submitted material.
b. The permitting authority will use the NMP to identify site-specific permit terms, to
be incorporated into this permit. The permitting authority will identify site-specific
permit terms with respect to protocols for the land application of manure, litter,
and process wastewater. The permitting authority will also identify site-specific
permit terms with respect to manure, litter, and process wastewater storage
capacities and site-specific conservation practices on the basis of the CAFO’s
NMP to the extent that such terms are necessary to support the application rates
expressed in the NMP. The permitting authority will also identify site-specific
permit terms with respect to mortality management, clean water diversions,
preventing direct contact of animals with waters of the United States, chemical
handling, protocols for manure and soil testing, and record keeping as appropriate.

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c. When the permitting authority determines that the NMP and NOI are complete,
the permitting authority will notify the public of the permitting authority’s
proposal to grant coverage under the permit and make available for public review
and comment the NOI submitted by the CAFO, including the CAFO’s NMP, and
the permitting authority will identify the terms of the NMP to be incorporated into
the permit. [The permit should state where and how notice to the public will be
provided.]
d. The period for the public to comment and request a hearing on the proposed
terms of the NMP to be incorporated into the permit shall be [The permitting
authority can specify in the permit; cite a state regulation; or use a time period
specified in 40 CFR part 124.10 (i.e., 30 days)].
e. The permitting authority will respond to comments received during the
comment period, as provided in 40 CFR part 124.17, and, if necessary, require the
CAFO owner or operator to revise the NMP to be granted permit coverage.
f. When the permitting authority authorizes the CAFO owner or operator to
discharge under the general permit, the terms of the NMP shall be incorporated
as terms and conditions of the permit for the CAFO. The permitting authority will
notify the CAFO owner or operator that coverage has been authorized and of the
applicable terms and conditions of the permit. Those site-specific permit terms
will be provided to the permittee in a [permitting authority specify procedure/
mechanism (e.g., permit authorization notice/letter, certificate of coverage,
permit modification)].
g. Each CAFO covered by this permit must comply with the site-specific permit
terms established by the permitting authority on the basis of the CAFO’s sitespecific NMP.
3. NMP Content. The site-specific NMP at a minimum must include practices and
procedures necessary to implement the applicable effluent limitations and standards
in Part II.A of this permit. In addition, the NMP and each CAFO covered by this permit
must, as applicable do the following:
a. Ensure adequate storage of manure, litter, and process wastewater, including
procedures to ensure proper operation and maintenance of the storage facilities.
All wastewater and manure containment structures shall at a minimum be
designed, constructed, operated, and maintained in accordance with the
standards of the Natural Resources Conservation Service, Field Office Technical
Guide [or other standards identified by the permitting authority]. Storage
capacity must be sufficient to meet the minimum applicable state requirements,
including [permitting authority specify or reference state storage requirements],
and it must be sufficient to allow the CAFO to comply with the land application
schedule specified in the NMP. The NMP must describe the extent that the NMP

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depends on off-site transport or other means of handling to ensure adequate
storage capacity, if applicable.

[If the CAFO needs to maintain storage capacity that exceeds the minimum
state capacity requirements to comply with the land application provisions
in the NMP, the storage capacity shall become a term of this permit and sitespecific terms are to be developed by the permitting authority on the basis of the
submitted NMP.]

b. Ensure proper management of mortalities (i.e., dead animals) to ensure that
they are not disposed of in a liquid manure, stormwater, or process wastewater
storage or treatment system that is not specifically designed to treat animal
mortalities. Mortalities shall be handled in such a way as to prevent the discharge
of pollutants to waters of the United States. Mortality handling practices shall be in
accordance with all applicable state and local regulatory requirements, including
[Insert state/local regulatory requirements as appropriate. Any such state/
local requirements should be consistent with NRCS Practice Standard 316 as
applicable.].
c. Ensure that clean water is diverted, as appropriate, from the production area.
Any clean water that is not diverted and comes into contact with raw materials,
products, or by-products including manure, litter, process wastewater, feed, milk,
eggs, or bedding is subject to the effluent limitations specified in Part II.A of this
permit. Where clean water is not diverted, the CAFO owner or operator must
document that it has been accounted for in meeting the requirement to ensure
adequate storage capacity as a condition of this permit. Clean water includes, but is
not limited to, rain falling on the roofs of facilities and runoff from adjacent land.
d. Prevent the direct contact of animals confined or stabled at the facility with waters
of the United States.
e. Ensure that chemicals and other contaminants handled on-site are not disposed
of in any manure, litter, process wastewater, or stormwater storage or treatment
system unless specifically designed to treat such chemicals or contaminants. All
wastes from dipping vats, pest and parasite control units, and other facilities used
for the management of potentially hazardous or toxic chemicals shall be handled
and disposed of in a manner sufficient to prevent pollutants from entering the
manure, litter, or process wastewater retention structures or waters of the United
States. Include references to any applicable chemical handling protocols and
indicate that other protocols included in the NMP will be reviewed.
f. Identify appropriate site-specific conservation practices to be implemented,
including as appropriate buffers or equivalent practices, to control runoff of
pollutants to waters of the United States and specifically to minimize the runoff
of nitrogen and phosphorus. Each CAFO covered by this permit must implement
the site-specific conservation practices determined by the permitting authority

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to be a term of this permit, as specified in [Identify mechanism (e.g., permit
authorization notice/letter, certificate of coverage, permit modification) that the
permitting authority will use to specify terms.], including residue management,
conservation crop rotation, grassed waterways, strip cropping, vegetated buffers,
riparian buffers, setbacks, terracing, and diversions. At a minimum, such practices
must be adequate to keep erosion levels in each field at or less than the soil loss
tolerance (T) value specified in the Natural Resources Conservation Service,
Field Office Technical Guide [or other standards identified by the Permitting
Authority]. [Comment: Note that conservation practices become terms of the
NMP in two ways:
i. Conservation practices are terms based on the information, protocols,
BMPs and activities deemed necessary to meet part 122.42(e)(1).
ii. Conservation practices become permit terms to the extent that they
influence the risk of runoff rating and consequently the application rate.
Site-specific terms are to be developed by the permitting authority based on
the submitted NMP.]
g. Identify protocols for appropriate testing of manure, litter, process wastewater, and
soil. Manure, wastewater and soil sampling must be conducted in accordance with
the requirements of Part III.A.2.b of this permit and the following protocols: [Insert
specific references for the protocols that are to be used].
h. Establish protocols to land apply manure, litter, or process wastewater in
accordance with site-specific nutrient management practices that ensure
appropriate agricultural utilization of the nutrients in the manure, litter, or process
wastewater.

The CAFO’s site-specific NMP shall document the calculation of land application
rates of manure, litter, or process wastewater. The following technical standard
for nutrient management established by the permitting authority shall be used
for calculating these rates. [Insert reference to state technical standards] The
rate calculation shall address the form, source, amount, timing, and method of
application on each field to achieve realistic production goals while minimizing
nitrogen and phosphorus movement to surface water. The rate calculation shall
be based on the results of a field specific assessment of the potential for nitrogen
and phosphorus transport from the field to surface waters using the following
assessment protocol [Insert phosphorus risk assessment tool established by the
permitting authority].

Application rates may be expressed in NMPs consistent with one of the two
approaches described in Parts III.A.3.h.i and ii of this permit. [The permitting
authority may limit CAFOs to one approach for specifying application rates or
allow both approaches.]

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Development of site-specific terms will be based on the permitting authority’s
review of the NMP submitted in accordance with the requirements of Part III.B of
this permit. To support the development of site-specific terms the submitted NMP
must include at a minimum:
• Names of fields available for land application.
• Field-specific rates of application properly developed as specified in paragraph
i or ii below in the following chemical forms in this part and [specify forms of
nitrogen and phosphors to be used for expressing application rates].
• [Placeholder for EPA-or state-specified timing restrictions such as no
saturated, frozen, or snow covered ground or during periods of crop
dormancy].
• The information specified in paragraph i and ii below for the selected approach.
• Any additional information necessary to assess the adequacy of the application
rates included in the NMP.
i. Linear Approach. Expresses rates of application as pounds of nitrogen
and phosphorus. CAFOs selecting the linear approach to address rates of
application must include in the NMP submitted to the permitting authority
the following information for each crop, field, and year covered by the NMP,
which will be used by the permitting authority to establish site-specific
permit terms:
• The maximum application rate (pounds/acre/year of nitrogen and
phosphorus) from manure, litter, and process wastewater.
• The outcome of the field-specific assessment of the potential for nitrogen
and phosphorus transport from each field. [If a state does not have an
N transport risk assessment, the NMP must document any basis for
assuming that nitrogen will be fully used by crops.] The CAFO must
specify any conservation practices used in calculating the risk rating.
• The crops to be planted or any other uses of a field such as pasture or
fallow fields.
• The realistic annual yield goal for each crop or use identified for each field.
• The nitrogen and phosphorus recommendations from [permitting
authority to specify acceptable sources] for each crop or use identified for
each field.
• Credits for all residual nitrogen in each field that will be plant-available.
• Consideration of multi-year phosphorus application. For any field where
nutrients are applied at a rate based on the crop phosphorus requirement,
the NMP must account for single-year nutrient applications that supply
more than the crop’s annual phosphorus requirement.

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• All other additions of plant available nitrogen and phosphorus (i.e., from
sources other than manure, litter, or process wastewater or credits for
residual nitrogen).
• The form and source of manure, litter, and process wastewater to be landapplied.
• The timing and method of land application. The NMP also must include
storage capacities needed to ensure adequate storage that accommodates
the timing indicated.
• The methodology that will be used to account for the amount of nitrogen
and phosphorus in the manure, litter, and wastewater to be applied.
• Any other factors necessary to determine the maximum application rate
identified in accordance with this Linear Approach.
ii. Narrative Rate Approach. Expresses a narrative rate of application that results
in the amount, in tons or gallons, of manure, litter, and process wastewater to
be land applied. CAFOs selecting the narrative rate approach to address rates
of application must include in the NMP submitted to the permitting authority
the following information for each crop, field, and year covered by the NMP,
which will be used by the permitting authority to establish site-specific
permit terms:
• The maximum amounts of nitrogen and phosphorus that will be derived
from all sources of nutrients (pounds/acre for each crop and field).
• The outcome of the field-specific assessment of the potential for nitrogen
and phosphorus transport from each field. [If a state does not have an
N transport risk assessment, the NMP must document any basis for
assuming that nitrogen will be fully used by crops.] The CAFO must
specify any conservation practices used in calculating the risk rating.
• The crops to be planted in each field or any other uses of a field such as
pasture or fallow fields, including alternative crops if applicable. Any
alternative crops included in the NMP must be listed by field, in addition
to the crops identified in the planned crop rotation for that field.
• The realistic annual yield goal for each crop or use identified for each field
for each year, including any alternative crops identified.
• The nitrogen and phosphorus recommendations from [the permitting
authority to specify acceptable sources] for each crop or use identified for
each field, including any alternative crops identified.
• The methodology (including formulas, sources of data, protocols for
making determination, etc.) and actual data that will be used to account
for: (1) the results of soil tests required by Parts II.A.4.b and III.A.3.g
of this permit, (2) credits for all nitrogen in the field that will be plant-

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available, (3) the amount of nitrogen and phosphorus in the manure,
litter, and process wastewater to be applied, (4) consideration of multiyear phosphorus application (for any field where nutrients are applied
at a rate based on the crop phosphorus requirement, the methodology
must account for single-year nutrient applications that supply more than
the crop’s annual phosphorus requirement), (5) all other additions of
plant available nitrogen and phosphorus to the field (i.e., from sources
other than manure, litter, or process wastewater or credits for residual
nitrogen), (6) timing and method of land application, and (7) volatilization
of nitrogen and mineralization of organic nitrogen.
• Any other factors necessary to determine the amounts of nitrogen
and phosphorus to be applied in accordance with the Narrative Rate
Approach.
• NMPs using the Narrative Rate Approach must also include the following
projections, which will not be used by the permitting authority in
establishing site-specific permit terms:
i. Planned crop rotations for each field for the period of permit
coverage.
ii. Projected amount of manure, litter, or process wastewater to be
applied.
iii. Projected credits for all nitrogen in the field that will be plantavailable.
iv. Consideration of multi-year phosphorus application.
v. Accounting for other additions of plant-available nitrogen and
phosphorus to the field.
vi. The predicted form, source, and method of application of manure,
litter, and process wastewater for each crop.
4. Signature. The NMP shall be signed by the owner/operator or other signatory authority
in accordance with Part VII.E of this permit (Signatory Requirements).
5. A current copy of the NMP shall be kept on site at the permitted facility in accordance
with Part VII.C of this permit and provided to the permitting authority upon request.
6. Recordkeeping Requirement
a. Large CAFOs using the linear rate approach must calculate the maximum amount
of manure, litter, and process wastewater to be land applied at least once each
year using the results of the most recent representative manure, litter, and process
wastewater tests of nitrogen and phosphors. Such representative test must be
taken within 12 months of the date of land application.

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b. All CAFOs using the narrative rate approach must calculate maximum amounts
of manure, litter, and process wastewater to be land applied at least once each
year using the methodology specified in the NMP pursuant to Part III.A.3.h of
this permit before land applying manure, litter, and process wastewater. Such
calculations must rely on the following data:
i. A field-specific determination of soil levels of nitrogen and phosphorus. For
nitrogen, the determination must include a concurrent determination of nitrogen
that will be plant available. For phosphorus, the determination must include the
results of the most recent soil test conducted as required in Parts II.A.4.b and
III.A.3.g of this permit.
ii. The results of the most recent representative manure, litter, and process
wastewater tests for nitrogen and phosphorus taken within 12 months of the date
of land application, as required in Parts II.A.4.b and III.A.3.g of this permit, in
order to determine the amount of nitrogen and phosphorus in the manure, litter,
and process wastewater to be applied.
c. Identify and maintain all records necessary to document the development and
implementation of the NMP and compliance with the permit.
7. Changes to the NMP
a. When a CAFO owner or operator covered by this permit makes changes to the
CAFO’s NMP previously submitted to the permitting authority, the CAFO owner
or operator must provide the permitting authority with the most current version
of the CAFO’s NMP and identify changes from the previous version, except
that annual calculations of application rates for manure, litter, and process
wastewater as required in Part III.A.6.a of this permit (for the Linear Approach) and
Part III.A.6.b of this permit (for the Narrative Rate Approach) are not required to be
submitted to the permitting authority.
b. When changes to an NMP are submitted to the permitting authority, the
permitting authority will review the revised NMP to ensure that it meets the
requirements of Parts II.A and III.A.3 of this permit. If the permitting authority
determines that the changes to the NMP necessitate revision to the terms of the
NMP incorporated into the permit issued to the CAFO, the permitting authority
must determine whether such changes are substantial. Substantial changes to the
terms of an NMP incorporated as terms and conditions of a permit include the
following:
i. Addition of new land application areas not previously included in the CAFO’s
NMP, except if the added land application area is covered by the terms of an NMP
incorporated into an existing NPDES permit and the CAFO complies with such
terms when applying manure, litter, and process wastewater to the added land.
ii. For NMPs using the Linear Approach, changes to the field-specific maximum
annual rates of land application (pounds of nitrogen and phosphorus from

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manure, litter, and process wastewater). For NMPs using the Narrative Rate
Approach, changes to the maximum amounts of nitrogen and phosphorus
derived from all sources for each crop.
iii. Addition of any crop or other uses not included in the terms of the CAFO’s NMP.
iv. Changes to site-specific components of the CAFO’s NMP, where such changes are
likely to increase the risk of nitrogen and phosphorus transport to waters of the
United States.
v. If the permitting authority determines that the changes to the terms of the NMP
are not substantial, the permitting authority will include the revised NMP in the
permit record, revise the terms of the permit on the basis of the site-specific NMP,
and notify the CAFO and the public of any changes to the terms of the permit on
the basis of revisions to the NMP.
vi. If the permitting authority determines that the changes to the terms of the
NMP are substantial, the permitting authority will notify the public, make
the proposed changes and the information submitted by the CAFO owner or
operator available for public review and comment, and respond to all significant
comments received during the comment period. The permitting authority may
require the CAFO to further revise the NMP, if necessary. Once the permitting
authority incorporates the revised terms of the NMP into the permit, the
permitting authority will notify the CAFO of the revised terms and conditions
of the permit. [The permitting authority can specify a period for processing
substantial changes and the permit should state where and how notice to the
public will be provided.]

B. Terms of The Nutrient Management Plan
Any CAFO authorized under this general permit must comply with the terms of the CAFO’s sitespecific NMP, as established by the permitting authority pursuant to the procedural requirements
of Part III.A of this permit. The terms of the NMP for each CAFO authorized by this permit are a
part of this permit and are set forth as follows:
[The permit must clearly establish that the terms of the NMP are enforceable terms and
conditions of the permit. In addition, the permitting authority must identify how the terms of
the NMP are documented and included or otherwise incorporated into the permit. Any permit
text must be part of the text of the permit as a whole. The location of the CAFO’s entire NMP
must also be identified so that the public can refer to the document as a whole.]
Permit Terms and Conditions
[In this section add the site-specific components of the NMP that are necessary to meet the
requirements of 40 CFR part 122.42(e)(5(i) or (ii)].

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Part IV. Special Conditions
A. Facility Closure
The following conditions shall apply to the closure of lagoons and other earthen or synthetic lined
basins and other manure, litter, or process wastewater storage and handling structures:
1. Closure of Lagoons and Other Surface Impoundments
a. No lagoon or other earthen or synthetic lined basin shall be permanently abandoned.
b. Lagoons and other earthen or synthetic lined basins shall be maintained at all
times until closed in compliance with this section.
c. All lagoons and other earthen or synthetic lined basins must be properly closed
if the permittee ceases operation. In addition, any lagoon or other earthen or
synthetic lined basin that is not in use for a period of 12 consecutive months must
be properly closed unless the facility is financially viable, intends to resume use
of the structure at a later date, and either (1) maintains the structure as though it
were actively in use, to prevent compromise of structural integrity; or (2) removes
manure and wastewater to a depth of one foot or less and refills the structure with
clean water to preserve the integrity of the synthetic or earthen liner. In either case,
the permittee shall notify the [Permitting Authority] of the action taken and
shall conduct routine inspections, maintenance, and record keeping as though the
structure were in use. Before restoration or use of the structure, the permittee shall
notify the [Permitting Authority] and provide the opportunity for inspection.
d. All closure of lagoons and other earthen or synthetic lined basins must be
consistent with [insert citation to specific standards as determined to be
applicable by the permitting authority]. Consistent with that standard, the
permittee shall remove all waste materials to the maximum extent practicable
and dispose of them in accordance with the permittee’s NMP, unless otherwise
authorized by the [Permitting Authority].
e. Unless otherwise authorized by the [Permitting Authority], completion of
closure for lagoons and other earthen or synthetic lined basins shall occur as
promptly as practicable after the permittee ceases to operate or, if the permittee
has not ceased operations, 12 months from the date on which the use of the
structure ceased, unless the lagoons or basins are being maintained for possible
future use in accordance with the requirements above.
2. Closure Procedures for Other Manure, Litter, or Process Wastewater Storage and
Handling Structure

No other manure, litter, or process wastewater storage and handling structure shall
be abandoned. Closure of all such structures shall occur as promptly as practicable
after the permittee has ceased to operate, or, if the permittee has not ceased to operate,
within 12 months after the date on which the use of the structure ceased. To close a

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manure, litter, or process wastewater storage and handling structure, the permittee
shall remove all manure, litter, or process wastewater and dispose of it in accordance
with the permittee’s NMP, or document its transfer from the permitted facility in
accordance with off-site transfer requirements specified in this permit [Insert Permit
Cite], unless otherwise authorized by the [Permitting Authority].

B. Additional Special Conditions
[This section is to be used by the permitting authority to specify any additional special
conditions such as procedures for emergency discharge impact abatement, irrigation
control, spill control procedures, specific measurements to be collected (i.e., rainfall), and
groundwater protection requirements (e.g., monitoring, liners) that are determined necessary
by the permitting authority.]

Part V. Discharge Monitoring and Notification
Requirements
A. Notification of Discharges Resulting from Manure, Litter,
and Process Wastewater Storage, Handling, On-site
Transport and Application
If, for any reason, there is a discharge of pollutants to waters of the United States, the permittee
is required to make immediate oral notification within 24 hours to the [Permitting Authority
(Contact Number)] and notify the [Permitting Authority] in writing within 5 working days
of the discharge from the facility. In addition, the permittee shall keep a copy of the notification
submitted to the [Permitting Authority] together with the other records required by this
permit. The discharge notification shall include the following information:
1. A description of the discharge and its cause, including a description of the flow path to
the receiving waterbody and an estimate of the flow and volume discharged.
2. The period of noncompliance, including exact dates and times, the anticipated time it
is expected to continue, and steps taken or planned to reduce, eliminate and prevent
recurrence of the discharge.

B. Monitoring Requirements for All Discharges from
Retention Structures
If any overflow or other discharge of pollutants occurs from a manure and/or wastewater storage
or retention structure, whether or not authorized by this permit, the [Permitee] shall take the
following actions:
1. All discharges shall be sampled and analyzed. Samples must, at a minimum, be
analyzed for the following parameters: total nitrogen, ammonia nitrogen phosphorus,

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fecal coliform, 5-day biochemical oxygen demand (BOD5), total suspended solids, pH,
and temperature. The discharge must be analyzed in accordance with approved EPA
methods for water analysis listed in 40 CFR Part 136. [The permitting authority may
specify additional parameters that are to be analyzed (e.g., metals).]
2. Record an estimate of the volume of the release and the date and time.
3. [The permitting authority should insert the specific procedures that are to be
followed by the permittee in collecting these samples. The permitting authority
should also specify the time frame for reporting the results of the analyses.] The
discharge must be collected in accordance with approved EPA methods for water
analysis listed in 40 CFR Part 136.
4. If conditions are not safe for sampling, the permittee must provide documentation of
why samples could not be collected and analyzed. For example, the permittee may
be unable to collect samples during dangerous weather conditions (such as local
flooding, high winds, hurricane, tornadoes, electrical storms, and such). However,
once dangerous conditions have passed, the permittee shall collect a sample from the
retention structure (pond or lagoon) from which the discharge occurred.

C. General Inspection, Monitoring, and Record-Keeping
Requirements
The permittee shall inspect, monitor, and record the results of such inspection and monitoring in
accordance with Table V–A.
Table V-A. NPDES Large CAFO Permit Record-Keeping Requirements
Parameter

Units

Frequency

Permit and Nutrient Management Plan
(Note: Required by the NPDES CAFO Regulation—applicable to all CAFOs)

The CAFO must maintain on-site a copy of the current NPDES
permit, including [specify mechanism to identify site-specific
terms].

N/A

Maintain at all
times

The CAFO must maintain on-site a current, site-specific NMP that
reflects existing operational characteristics. The operation must
also maintain on-site all necessary records to document that the
NMP is being properly implemented with respect to manure
and wastewater generation, storage and handling, and land
application. In addition, records must be maintained that the
development and implementation of the NMP is in accordance
with the minimum practices defined in 40 CFR part 122.42(e).

N/A

Maintain at all
times

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Table V-A. NPDES Large CAFO Permit Record-Keeping Requirements (continued)
Parameter

Units

Frequency

Soil and Manure/Wastewater Nutrient Analysis

(Note: Required by the CAFO ELG —applicable to Large CAFOs)

Analysis of manure, litter, and process wastewater to determine
nitrogen and phosphorus content.a

ppm

Analysis of soil in all fields where land application activities are
conducted to determine phosphorus content.a

ppm

Pounds/ton

At least
annually after
initial sampling
At least once
every 5 years
after initial
sampling

Operation and Maintenance (Note: Required by the CAFO ELG —applicable to Large CAFOs)
Visual inspection of all water lines

N/A

Dailyb

Documentation of depth of manure and process wastewater in all
liquid impoundments

Feet

Weekly

Documentation of all corrective actions taken. Deficiencies
not corrected within 30 days must be accompanied by an
explanation of the factors preventing immediate correction.

N/A

As necessary

Operation and Maintenance (Note: Required by the CAFO ELG —applicable to Large CAFOs)
Documentation of animal mortality handling practices

N/A

As necessary

Design documentation for all manure, litter, and wastewater storage structures including the
following information:
• Volume for solids accumulation

Cubic yards/
gallons

Once in the
permit

• Design treatment volume

Cubic yards/
gallons

term unless
revised

• Total design storage volumec

Cubic yards/
gallons

• Days of storage capacity

Days

Documentation of all overflows from all manure and wastewater storage structures including:
(Note: Required by the NPDES Regulation —applicable to all CAFOs)

• Date and time of overflow
• Estimated volume of overflow
• Analysis of overflow (as required by the permitting
authority)

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Month/day/
year

Per event

Total gallons

Per event

TBD

Per event

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Table V-A. NPDES Large CAFO Permit Record-Keeping Requirements (continued)
Parameter

Units

Frequency

Land Application (Note: Required by the CAFO ELG —applicable to Large CAFOs)
For each application event where manure, litter, or process wastewater is applied, documentation of
the following by field:
• Date of application

Month/day/
year

Daily

• Weather conditions at the time of application and for
24 hours before and after application

N/A

Daily

• Total amount of nitrogen and phosphorus appliedd

Pounds/acre

Daily

Documentation of the crop and expected yield for each field

Bushel/acre

Seasonally

Documentation of the actual crop planted and actual yield for
each field

Bushel/acre

Seasonally

Documentation of test methods and sampling protocols used to
sample and analyze manure, litter, and wastewater and soil.

N/A

Once in the
permit term
unless revised

Documentation of the basis for the application rates used for
each field where manure, litter, or wastewater is applied.

N/A

Once in the
permit term
unless revised

Documentation showing the total nitrogen and phosphorus to be
applied to each field including nutrients from the application of
manure, litter, and wastewater and other sources

Pounds/acre

Once in the
permit term
unless revised

Documentation of manure application equipment inspection

N/A

Seasonally

• Method of application

Daily

N/A

Manure Transfer (Note: Required by the NPDES CAFO Regulation—applicable to Large CAFOs)
For all manure transfers the CAFO must maintain the following records:
• Date of transfer

N/A

As necessary

• Name and address of recipient

N/A

As necessary

• Approximate amount of manure, litter, or wastewater
transferred

Tons/gallons

As necessary

Notes:
a. For the specific analyses to be used, see the state nutrient management technical standard.
b. Visual inspections should take place daily during the course of normal operations. The completion of such
inspection should be documented in a manner appropriate to the operation. Some operations might wish to
maintain a daily log. Other operations might choose to make a weekly entry, when they update other weekly
records that required daily inspections have been completed.
c. Total design volume includes normal precipitation less evaporation on the surface of the structure for the
storage period, normal runoff from the production area for the storage period, 25-year, 24-hour precipitation
on the surface of the structure, 25-year, 24-hour runoff from the production area, and residual solids.
d. Including quantity/volume of manure, litter, or process wastewater applied and the basis for the rate of
phosphorus application.

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D. Additional Monitoring Requirements
[This section is to be used by the permitting authority to specify any additional monitoring
and analysis that the permittee is to perform.]
1. Additional monitoring for some high risk operations: Upon notification by
[Permitting Authority], the permittee may be required to conduct ambient
monitoring of surface or groundwater or both. For example, facilities with
historical compliance problems, especially large facilities, facilities with significant
environmental concerns, or facilities impacting impaired waterbodies. [The
permitting authority should establish appropriate ambient surface and
groundwater monitoring requirements in the NPDES permit.]
2. Upon request by [Permitting Authority], the permittee may be required to collect
and analyze samples including but not limited to soils, surface water, groundwater, or
stored waste in a manner and frequency specified by [Permitting Authority].

Part VI. Annual Reporting Requirements
[This example permit includes the minimum information required by the NPDES regulations.
The permitting authority can use its discretion concerning additional information required to
be submitted with the annual report.]
A. The permittee must submit an annual report to the permitting authority by [Date] of
each year.
B. The annual report must include the following information:
[The permitting authority can use its discretion and authority to request additional
information from the permittee. The permitting authority might wish to provide an
example of the specific format for the annual report. An example report is included
in the NPDES CAFO Permit Writer Guidance.]
1. The number and type of animals, whether in open confinement or housed under roof.
2. Estimated amount of total manure, litter, and process wastewater generated by the
CAFO in the previous 12 months (tons/gallons).
3. Estimated amount of total manure, litter, and process wastewater transferred to other
person by the CAFO in the previous 12 months (tons/gallons).
4. Total number of acres for land application covered by the NMP.
5. Total number of acres under control of the CAFO that were used for land application of
manure, litter, and process wastewater in the previous 12 months.
6. Summary of all manure, litter, and process wastewater discharges from the production
area that have occurred in the previous 12 months, including date, time, and
approximate volume.

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7. A statement indicating whether the current version of the CAFO’s NMP was developed
or approved by a certified nutrient management planner.
8. Actual crops planted and actual yields for each field for the preceding 12 months.
9. Results of all samples of manure, litter or process wastewater for nitrogen and
phosphorus content for manure, litter and process wastewater that was land applied.
10. Results of calculations conducted in accordance with Part III.A.6.a of this permit
(for the Linear Approach) and Part III.A.6.b of this permit (for the Narrative Rate
Approach).
11. Amount of manure, litter, and process wastewater applied to each field during the
preceding 12 months.
12. For CAFOs using the Narrative Rate Approach to address rates of application:
i. The results of any soil testing for nitrogen and phosphorus conducted during the
preceding 12 months.
ii. The data used in calculations conducted in accordance with Part III.A.3.h of this
permit.
iii. The amount of any supplemental fertilizer applied during the preceding 12 months.

Part VII. Standard Permit Conditions
A. General Conditions
1. In accordance with the provisions of 40 CFR Part 122.41 et. seq., this permit incorporates by reference all conditions and requirements applicable to NPDES Permits set
forth in the Clean Water Act, as amended, (the Act) and all applicable regulations.
2. The permittee must comply with all conditions of this permit. Any permit
noncompliance constitutes a violation of the Act and is grounds for enforcement
action; for permit termination, revocation, and reissuance; for denial of a permit
renewal application; and/or for requiring a permittee to apply for and obtain an
individual NPDES permit.
3. The permittee shall comply with effluent standards and prohibitions established under
section 307(a) of the Act for toxic pollutants within the time provided in the regulations
that establish those standards or prohibitions, even if the permit has not yet been
modified to incorporate the requirement.
4. This permit may be modified, revoked and reissued, or terminated for cause. The filing
of a request for a permit modification, revocation and reissuance, or termination, or
a notification of planned changes or anticipated noncompliance, does not stay any
permit condition.

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5. The issuance of this permit does not convey any property rights of any sort, or any
exclusive privileges, nor does it authorize any injury to private property or any
invasion of personal rights, nor any infringement of federal, state/tribal or local laws or
regulations.
6. The permittee shall furnish to the permitting authority, within a reasonable time,
any information that the permitting authority might request to determine whether
cause exists for modifying, revoking and reissuing, or terminating this permit, or
to determine compliance with this permit. The permittee shall also furnish to the
permitting authority, on request, copies of records required to be kept by this permit.
7. Nothing in this permit shall be construed to relieve the permittee from civil
or criminal penalties for noncompliance. Any false or materially misleading
representation or concealment of information required to be reported by the
provisions of the permit, the Act, or applicable regulations, which avoids or effectively
defeats the regulatory purpose of the permit may subject the permittee to criminal
enforcement pursuant to 18 U.S.C. 1001.
8. Nothing in this permit shall be construed to preclude the institution of any legal action
or relieve the permittee from any responsibilities, liabilities, or penalties established
pursuant to any applicable state/tribal law or regulation under authority preserved by
section 510 of the Act.
9. The provisions of this permit are severable, and if any provision of this permit or the
application of any provision of this permit to any circumstance, is held invalid, the
application of such provision to other circumstances, and the remainder of this permit,
shall not be affected thereby.
10. Bypass
a. Definitions
i. Bypass means the intentional diversion of waste streams from any portion of a
treatment facility.
ii. Severe property damage means substantial physical damage to property, damage
to the treatment facilities that causes them to become inoperable, or substantial
and permanent loss of natural resources that can reasonably be expected
to occur in the absence of a bypass. Severe property damage does not mean
economic loss caused by delays in production.
b. Bypass not exceeding limitations. The permittee may allow any bypass to occur that
does not cause effluent limitations to be exceeded but only if it also is for essential
maintenance to assure efficient operation. Those bypasses are not subject to Parts
VII.A.10.c. and 10.d.of this permit.
c. Notice

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i. Anticipated bypass. If the permittee knows in advance of the need for a bypass, it
shall submit prior notice, if possible at least 10 days before the date of the bypass.
ii. Unanticipated bypass. The permittee shall submit notice of unanticipated bypass
as required Part VII.D.5.of this permit (24-hour notice).
d. Prohibitions of bypass.
i. Bypass is prohibited, and the permitting authority may take enforcement action
against a permittee for bypass, unless the following are true:
• Bypass was unavoidable to prevent loss of life, personal injury, or severe
property damage.
• There were no feasible alternatives to the bypass, such as the use of auxiliary
treatment facilities, retention of untreated wastes, or maintenance during
normal periods of equipment downtime. That condition is not satisfied if
adequate backup equipment should have been installed in the exercise of
reasonable engineering judgment to prevent a bypass that occurred during
normal periods of equipment downtime or preventive maintenance.
• The permittee submitted notices as required under Part VII.A.10.c of this
permit.
ii. The permitting authority may approve an anticipated bypass, after considering
its adverse effects, if the permitting authority determines that it will meet the
three conditions listed above in Part VII.A.10.d.(i) of this permit.
11. Upset
a. Definition. Upset means an exceptional incident in which there is unintentional
and temporary noncompliance with technology-based permit effluent limitations
because of factors beyond the reasonable control of the permittee. An upset does
not include noncompliance caused by operational error, improperly designed
treatment facilities, lack of preventive maintenance, or careless or improper
operation.
b. Effect of an upset. An upset constitutes an affirmative defense to an action brought
for noncompliance with such technology-based permit effluent limitations if the
requirements of Part VII.A.11.c. of this permit are met.
c. Conditions necessary for a demonstration of upset. A permittee who wishes to
establish the affirmative defense of upset shall demonstrate, through properly
signed, contemporaneous operating logs, or other relevant evidence of the following:
i. An upset occurred and that the permittee can identify the cause(s) of the upset.
ii. The permitted facility was at the time being properly operated.

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iii. The permittee submitted notice of the upset as required in Part VII.D.5 of this
permit (24-hour notice).
iv. The permittee complied with any remedial measures required under
Part VII.A.14 of this permit (duty to mitigate).
d. Burden of proof. In any enforcement proceeding, the permittee seeking to establish
the occurrence of an upset has the burden of proof.
12. Duty to reapply. If the permittee wishes to continue an activity regulated by this permit
after the expiration date of this permit, the permittee must apply for and obtain a new
permit.
13. Need to halt or reduce activity not a defense. It shall not be a defense for a permittee
in an enforcement action that it would have been necessary to halt or reduce the
permitted activity to maintain compliance with the conditions of this permit.
14. Duty to mitigate. The permittee shall take all reasonable steps to minimize or prevent
any discharge or sludge use or disposal in violation of this permit, which has a
reasonable likelihood of adversely affecting human health or the environment.
15. Inspection and entry. The permittee shall allow the permitting authority, or
an authorized representative (including an authorized contractor acting as a
representative of the permitting authority), upon presentation of credentials and other
documents as may be required by law, to do the following:
a. Enter the permittee’s premises where a regulated facility or activity is located or
conducted, or where records must be kept under the conditions of this permit.
b. Have access to and copy, at reasonable times, any records that must be kept under
the conditions of this permit.
c. Inspect at reasonable times any facilities, equipment (including monitoring and
control equipment), practices, or operations regulated or required under this permit.
d. Sample or monitor at reasonable times, for the purposes of assuring permit
compliance or as otherwise authorized by the Act, any substances or parameters at
any location.

B. Proper Operation and Maintenance
The permittee shall, at all times, properly operate and maintain all facilities and systems of
treatment and control (and related appurtenances) that are installed or used by the permittee
to achieve compliance with the conditions of this permit. Proper operation and maintenance
includes the operation of backup or auxiliary facilities or similar systems only when necessary to
achieve compliance with the conditions of the permit.

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C. Monitoring and Records
1. Samples and measurements taken for the purpose of monitoring shall be
representative of the monitored activity.
2. The permittee shall retain records of all monitoring information, including all
calibration and maintenance records and all original strip chart recordings for
continuous monitoring instrumentation, copies of all reports required by this permit,
and records of all data used to complete the application for this permit, for a period of
at least 5 years from the date of the sample, measurement, report, or application. That
period may be extended by request of the permitting authority at any time.
3. Records of monitoring information shall include the following:
a. The date, exact place, and time of sampling or measurements.
b. The individual(s) who performed the sampling or measurements.
c. The date(s) analyses were performed.
d. The individual(s) who performed the analyses.
e. The analytical techniques or methods used.
f. The results of such analyses.
4. The permittee shall follow the following monitoring procedures:
a. Any required monitoring must be conducted according to test procedures
approved under 40 CFR Part 136, unless other test procedures have been specified
in this permit or approved by the Regional Administrator.
b. The permittee shall calibrate and perform maintenance procedures on all
monitoring and analytical instruments at intervals frequent enough to ensure
accuracy of measurements and shall maintain appropriate records of such
activities.
c. An adequate analytical quality control program, including the analyses of
sufficient standards, spikes, and duplicate samples to ensure the accuracy of all
required analytical results shall be maintained by the permittee or designated
commercial laboratory.
5. INSERT MONITORING REPORTS STANDARD CONDITION 40 CFR part 122.41(l)(4)
HERE.

D. Reporting Requirements
1. The permittee shall give notice to the permitting authority as soon as possible of any
planned physical alterations or additions to the permitted facility. Notice is required
only when any of the following are true:
a. The alteration or addition to a permitted facility may meet one of the criteria for
determining whether a facility is a new source in 40 CFR part 122.29(b).

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b. The alteration or addition could significantly change the nature or increase
the quantity of pollutants discharged. The notification applies to pollutants
that are subject neither to effluent limitations in the permit, nor to notification
requirements under 40 CFR 122.42(a)(1).
c. The alteration or addition results in a significant change in the permittee’s manure
use or disposal practices, and such alteration, addition, or change could justify the
application of permit conditions that are different from or absent in the existing
permit, including notification of additional use or disposal sites not reported
during the permit application process or not reported pursuant to an NMP.
2. The permittee shall give advance notice to the [Permitting Authority] of any
planned physical alterations or additions or changes in activity that could result in
noncompliance with requirements in this permit.
3. This permit is not transferable to any person except after notice to the [Permitting
Authority]. The [Permitting Authority] may require modification or revocation
and reissuance of the permit to change the name or the permittee and incorporate
such other requirements as might be necessary under the Act.
4. Reports of compliance or noncompliance with, or any progress reports on, interim
and final requirements contained in any compliance schedule of this permit shall be
submitted no later than 14 days following each scheduled date.
5. The permittee shall report any noncompliance that could endanger human health
or the environment. Any information must be provided orally to [Permitting
Authority Contact Information] within 24 hours from the time that the permittee
becomes aware of the circumstances. A written submission shall also be provided to
[Permitting Authority] within 5 days of the time the permittee becomes aware of
the circumstances. The report shall contain the following information:
a. A description of the noncompliance and its cause.
b. The period of noncompliance, including exact dates and times, and if the
noncompliance has not been corrected, the anticipated time it is expected to
continue.
c. Steps taken or planned to reduce, eliminate, and prevent recurrence of the
noncompliance.
6. The following shall be included as information, which must be reported within 24
hours:
a. Any unanticipated bypass that exceeds any effluent limitation in the permit.
b. Any upset that exceeds any effluent limitation in the permit.
c. Violation of a maximum daily discharge limitation for any of the pollutants listed
by the permitting authority in the permit to be reported within 24 hours.

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The permitting authority may waive the written report on a case-by-case basis for
reports under the above if the oral report has been received within 24 hours.

7. The permittee shall report all instances of noncompliance not reported under above
and of this section, at the time monitoring reports are submitted. The reports shall
contain the information listed in Part VII.D.6of this permit.
8. Where the permittee becomes aware that it failed to submit any relevant facts in a
permit application, or submitted incorrect information in a permit application or in
any report to the [Permitting Authority], the permittee shall promptly submit such
facts or information to the [Permitting Authority].

E. Signatory Requirements
All applications, reports, or information submitted to the [Permitting Authority] shall be
signed and certified consistent with 40 CFR part 122.22:
1. All notices of intent shall be signed as follows:
a. For a corporation: By a responsible corporate officer. For the purpose of this
section, a responsible corporate officer means either of the following:
i. A president, secretary, treasurer, or vice-president of the corporation in charge of
a principal business function, or any other person who performs similar policy or
decision-making functions for the corporation.
ii. The manager of one or more manufacturing, production, or operating facilities,
provided, the manager is authorized to make management decisions that govern
the operation of the regulated facility including having the explicit or implicit
duty of making major capital investment recommendations, and initiating and
directing other comprehensive measures to assure long-term environmental
compliance with environmental laws and regulations; the manager can ensure
that the necessary systems are established or actions taken to gather complete
and accurate information for permit application requirements; and where
authority to sign documents has been assigned or delegated to the manager in
accordance with corporate procedures.
b. For a partnership or sole proprietorship: By a general partner for a partnership or
the proprietor, respectively.
2. All reports required by the permit and other information requested by the
[Permitting Authority] shall be signed by a person described above or by a duly
authorized representative of that person. A person is a duly authorized representative
only if the following are true:
a. The authorization is made in writing by a person described above.
b. The authorization specifies either an individual or a position having responsibility
for the overall operation of the regulated facility or activity, such as the position of

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plant manager, operator of a well or a well field, superintendent, position of equiva­
lent responsibility, or any individual or position having overall responsibility for
environmental matters for the company. A duly authorized representative may
thus be either a named individual or an individual occupying a named position.
c. The written authorization is submitted to the [Permitting Authority].

F. Certification
Any person signing a document under this section shall make the following certification:
“I certify under penalty of law that this document and all attachments were prepared under
my direction or supervision in accordance with a system designed to assure that qualified
personnel properly gather and evaluate the information submitted. Based on my inquiry
of the person or persons who manage the system, or those persons directly responsible
for gathering the information, the information submitted is, to the best of my knowledge
and belief, true, accurate, and complete. I am aware that there are significant penalties
for submitting false information, including the possibility of fine and imprisonment for
knowing violations.”

G. Availability of Reports
Any information submitted pursuant to this permit may be claimed as confidential by the
submitter. If no claim is made at the time of submission, information may be made available to
the public without further notice.

H. Penalties for Violations of Permit Conditions
1. Criminal Penalties:
a. Negligent violations: The Act provides that any person who negligently violates
section 301, 302, 306, 307, 308, 318, or 405 of the Act or any condition or limitation
implementing those provisions in a permit issued under section 402 is subject
to a fine of not less than $2,750 nor more than $27,500 per day of violation, or by
imprisonment for not more than one year, or both.
b. Knowing violations: The Act provides that any person who knowingly violates
sections 301, 302, 306, 307, 308, 318, or 405 of the Act or any permit conditions imple­
menting those provisions is subject to a fine of not less than $5,500 nor more than
$55,000 per day of violation, or by imprisonment for not more than 3 years, or both.
c. Knowing endangerment: The Act provides that any person who knowingly violates
sections 301, 302, 303, 306, 307, 308, 318, or 405 of the Act or permit conditions
implementing those provisions and who knows at that time that he or she is
placing another person in imminent danger of death or serious bodily injury is

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subject to a fine of not more than $275,000, or by imprisonment for not more than
15 years, or both.
d. False statements: The Act provides that any person who knowingly makes any
false material statement, representation, or certification in any application, record,
report, plan, or other document filed or required to be maintained under the Act
or who knowingly falsifies, tampers with, or renders inaccurate, any monitoring
device or method required to be maintained under the Act, shall upon conviction,
be punished by a fine of not more than $11,000, or by imprisonment for not more
than 2 years, or by both. If a conviction of a person is for a violation committed
after a first conviction of such person under this paragraph, punishment shall be
by a fine of not more than $22,000 per day of violation, or by imprisonment of not
more than 4 years, or by both. [See section 309(c)4 of the Clean Water Act.]
2. Civil penalties: The Act provides that any person who violates a permit condition
implementing sections 301, 302, 306, 307, 308, 318, or 405 of the Act is subject to a civil
penalty not to exceed $27,500 per day for each violation. [See section 309(d).]
3. Administrative penalties: The Act provides that the Administrator may assess a Class I
or Class II administrative penalty if the Administrator finds that a person has violated
sections 301, 302, 306, 307, 308, 318, or 405 of the Act or a permit condition or limitation
implementing these provisions, as follows [See section 309(g).]:
a. Class I penalty: Not to exceed $11,000 per violation nor shall the maximum amount
exceed $27,500.
b. Class II penalty: Not to exceed $11,000 per day for each day during which the
violation continues nor shall the maximum amount exceed $137,500.

Part VIII. Definitions
Animal feeding operation means a lot or facility (other than an aquatic animal production
facility) where the following conditions are met: (i) animals (other than aquatic animals) have
been, are, or will be stabled or confined and fed or maintained for a total of 45 days or more in
any 12-month period, and (ii) crops, vegetation, forage growth, or post-harvest residues are not
sustained in the normal growing season over any portion of the lot or facility.
Application means the U.S. Environmental Protection Agency standard national forms for
seeking coverage under for an NPDES permit, including any additions, revisions or modifications
to the forms; or forms approved by U.S. Environmental Protection Agency for use in approved
states, including any approved modifications or revisions [e.g. for NPDES general permits, a
written NOI pursuant to 40 CFR part 122.28; for NPDES individual permits, Form 1 and 2B
pursuant to 40 CFR part 122.1(d)].
Concentrated animal feeding operation (CAFO) means an AFO that is defined as a Large CAFO
or Medium CAFO by 40 CFR parts 122.23 (4) and (6), or that is designated as a CAFO.

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Fecal coliform means the bacterial count (Parameter 1 at 40 CFR part 136.3 in Table 1A), which
also cites the approved methods of analysis.
Grab sample means a sample that is taken from a wastestream on a one-time basis without
consideration of the flow rate of the wastestream and without consideration of time.
Land application means the application of manure, litter, or process wastewater onto or
incorporated into the soil.
Land application area means land under the control of a CAFO owner or operator, whether it is
owned, rented, or leased, to which manure, litter, or process wastewater from the production area
is or could be applied.
Large CAFO means an AFO that stables or confines as many as or more than the numbers of
animals specified in any of the following categories: (i) 700 mature dairy cattle, whether milked
or dry; (ii)1,000 veal calves; (iii)1,000 cattle other than mature dairy cows or veal calves. Cattle
includes but is not limited to heifers, steers, bulls and cow/calf pairs; (iv) 2,500 swine each
weighing 55 pounds or more; (v)10,000 swine each weighing less than 55 pounds; (vi) 500 horses;
(vii) 10,000 sheep or lambs; (viii) 55,000 turkeys; (ix) 30,000 laying hens or broilers, if the AFO uses
a liquid manure handling system; (x)125,000 chickens (other than laying hens), if the AFO uses
other than a liquid manure handling system; (xi) 82,000 laying hens, if the AFO uses other than
a liquid manure handling system; (xii) 30,000 ducks (if the AFO uses other than a liquid manure
handling system); or (xiii) 5,000 ducks (if the AFO uses a liquid manure handling system).
Liquid manure handling system means a system that collects and transports or moves waste
material with the use of water, such as in washing pens and flushing confinement facilities. That
includes the use of water impoundments for manure or wastewater treatment.
Manure is defined to include manure, litter, bedding, compost and raw materials or other
materials commingled with manure or set aside for land application or other use.
Medium CAFO means any AFO that stables or confines as many or more than the numbers of
animals specified in any of the following categories: (i) 200 to 699 mature dairy cattle, whether
milked or dry cows; (ii) 300 to 999 veal calves; (iii) 300 to 999 cattle other than mature dairy cows
or veal calves. Cattle includes but is not limited to heifers, steers, bulls and cow/calf pairs; (iv) 750
to 2,499 swine each weighing 55 pounds or more; (v) 3,000 to 9,999 swine each weighing less
than 55 pounds; (vi)150 to 499 horses, (vii) 3,000 to 9,999 sheep or lambs, (viii) 16,500 to 54,999
turkeys, (ix) 9,000 to 29,999 laying hens or broilers, if the AFO uses a liquid manure handling
system; (x) 37,500 to 124,999 chickens (other than laying hens), if the AFO uses other than a liquid
manure handling system; (xi) 25,000 to 81,999 laying hens, if the AFO uses other than a liquid
manure handling system; (xii) 10,000 to 29,999 ducks (if the AFO uses other than a liquid manure
handling system); or (xiii) 1,500 to 4,999 ducks (if the AFO uses a liquid manure handling system)
and either one of the following conditions are met (a) pollutants are discharged into waters of the
United States through a man-made ditch, flushing system, or other similar man-made device; or

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(b) pollutants are discharged directly into waters of the United States that originate outside and
pass over, across, or through the facility or otherwise come into direct contact with the animals
confined in the operation.
Notice of Intent (NOI) is a form submitted by the owner/operator applying for coverage under
a general permit. It requires the applicant to submit the information necessary for adequate
program implementation, including, at a minimum, the legal name and address of the owner or
operator, the facility name and address, type of facility or discharges, and the receiving stream(s).
40 CFR § 128.28(b)(2)(ii).
Process wastewater means water directly or indirectly used in the operation of the CAFO for any
or all of the following: spillage or overflow from animal or poultry watering systems; washing,
cleaning, or flushing pens, barns, manure pits, or other AFO facilities; direct contact swimming,
washing, or spray cooling of animals; or dust control. Process wastewater also includes any
water that comes into contact with or is a constituent of raw materials, products, or by-products
including manure, litter, feed, milk, eggs, or bedding.
Production area means that part of an AFO that includes the animal confinement area,
the manure storage area, the raw materials storage area, and the waste containment areas.
The animal containment area includes but is not limited to open lots, housed lots, feedlots,
confinement houses, stall barns, free stall barns, milk rooms, milking centers, cowyards,
barnyards, medication pens, walkers, animal walkways, and stables. The manure storage area
includes but is not limited to lagoons, runoff ponds, storage sheds, stockpiles, under house
or pit storages, liquid impoundments, static piles, and composting piles. The raw materials
storage area includes but is not limited to feed silos, silage bunkers, and bedding materials. The
waste containment area includes but is not limited to settling basins, and areas within berms
and diversions that separate uncontaminated stormwater. Also included in the definition of
production area is any egg washing or egg processing facility, and any area used in the storage,
handling, treatment, or disposal of mortalities.
Small CAFO means an AFO that is designated as a CAFO and is not a Medium CAFO.
Setback means a specified distance from waters of the United States or potential conduits to
waters of the United States where manure, litter, and process wastewater may not be land applied.
Examples of conduits to surface waters include open tile line intake structures, sinkholes, and
agricultural well heads.
The Act means Federal Water Pollution Control Act as amended, also known as the Clean Water
Act as amended, found at 33 U.S.C. 1251 et seq.
Vegetated buffer means a narrow, permanent strip of dense perennial vegetation established
parallel to the contours of and perpendicular to the dominant slope of the field for the purposes
of slowing water runoff, enhancing water infiltration, and minimizing the risk of any potential
nutrients or pollutants from leaving the field and reaching waters of the United States.

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Waters of the United States means (1) all waters that are used, were used in the past, or might be
susceptible to use in interstate or foreign commerce, including all waters that are subject to the
ebb and flow of the tide; (2) all interstate waters, including interstate wetlands; (3) all other waters
such as intrastate lakes, rivers, and streams (including intermittent streams), mudflats, sandflats,
wetlands, sloughs, prairie potholes, wet meadows, playa lakes, or natural ponds the use,
degradation, or destruction of which would affect or could affect interstate or foreign commerce
including any such waters: (a) that are or could be used by interstate or foreign travelers for
recreational or other purposes; from which fish or shellfish are or could be taken and sold in
interstate or foreign commerce; or that are or could be used for industrial purposes by industries
in interstate commerce; (4) all impoundments of waters otherwise defined as waters of the United
States; (5) tributaries of waters identified in (1) through (4) of this definition; (6) the territorial sea;
and (7) wetlands adjacent to waters (other than waters that are themselves wetlands) identified in
items (1) through (6) of this definition.

Appendix A. (Insert Form 2B/Notice of Intent or Appropriate State
Form)
Appendix B. (Insert State Technical Standards for Nutrient
Management)
Appendix C. Historic Properties Requirements
Appendix D. Notice of Termination

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NPDES Permit Writers’ Manual for CAFOs

Appendix
NRCS Conservation
Practice Standards

K

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U.S. Department of Agriculture, Natural Resources
Conservation Service Conservation (USDA-NRCS)
Practice Standards
This appendix describes selected conservation practice standards developed by USDA-NRCS
that NPDES permit writers and inspectors might encounter in their review of CAFO nutrient
management plans. USDA-NRCS maintains the most recent national version of many of the
standards along with their associated job sheets and statements of work in its National Handbook
of Conservation Practice Standards (available at
http://www.nrcs.usda.gov/Technical/Standards/nhcp.html).
Each state’s NRCS office adopts and may modify those practices that are applicable in that state.
Some state NRCS offices also develop state-specific standards that are not found in the national
handbook. NPDES permit writers and inspectors should refer to the practice standards that are
applicable in their state. All state-specific conservation practice standards are available in the
Electronic Field Office Technical Guide (eFOTG, available at http://www.nrcs.usda.gov/technical/
efotg/). To find a specific standard, use the interactive maps on eFOTG to select the appropriate
state and county. Then select Section IV from the menu at the left side of the screen for a list of
practice standards available in that state.

Conservation Practice: Access Control (Code 472)

Application: Production Area
Barriers can be used to prevent, restrict, or control access to an area to maintain or improve
the quantity and quality of natural resources or to minimize liability and human health
concerns. Barriers consist of natural or artificial structures such as logs, vegetation, earth
fill, boulders, fences, gates, electronic and sonic devices, and signs. In those cases where
a waterbody is present in the feedlot area of the operation, the NMP should address the
installation and maintenance of a fence, or similar barrier, to prevent animals from
entering the water. In addition, the slope of the feedlot should be contoured to divert runoff
away from the waterbody.

Conservation Practice: Access Road (Code 560)

Application: Production Area
The standard establishes a travel-way for equipment and vehicles constructed as part of a
conservation plan.
The purpose of this practice is to provide a fixed route for vehicular travel for resource
activities involving the management of timber, livestock, agriculture, wildlife habitat, and
other conservation enterprises while protecting the soil, water, air, fish, wildlife, and other
adjacent natural resources where access is needed from a private or public road or highway
to a land use enterprise or conservation measure, or where travel ways are needed in a
planned land use area.

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Access roads range from seasonal use roads, designed for low speed and rough driving
conditions, to all-weather roads heavily used by the public and designed with safety as a
high priority. Some roads are constructed for a single purpose only; i.e., control of forest
fires, logging and forest management activities, access to remote recreation areas, or access
for maintenance of facilities.
Access roads should be located so as to minimize adverse effects on wetlands, waterbodies,
wildlife habitat, and air quality. Considerations should be given to the following:
▶ Effects on downstream flows or aquifers that would affect other water uses or users.
▶ Effects on the volume and timing of downstream flow to prohibit undesirable
environmental, social or economic effects.
▶ Short-term and construction-related effects of this practice on the quality of on-site
downstream water courses.
▶ Overall effects on erosion and the movement of sediment, pathogens, and soluble
and sediment-attached substances that would be carried by runoff from construction
activities.
▶ Effects on wetlands and water-related wildlife habitats that would be associated with
the practice.
▶ Establishing vegetation on road shoulders wider than 2-4 feet.
▶ Limiting the number of vehicles and vehicle speed will reduce the potential for
generation of particulate matter and decease safety and air quality concerns.

Conservation Practice: Agrichemical Handling Facility (Code 309)

Application: Production Area
An agrichemical handling facility has an impervious surface to provide a safe
environment on farm and ranch operations for the storage, mixing, loading and cleanup
of agrichemicals. The practice is also used to retain incidental spillage, retain leakage, and
reduce pollution to surface water, groundwater, air, and/or soil.
The practice applies where
▶ The handling of agrichemicals creates significant potential for pollution of surface
water, groundwater, air or soil and a facility is needed to properly manage and handle
the chemical operation.
▶ An adequate water supply is available for filling application equipment tanks, rinsing
application equipment and chemical containers as needed for the operation.
▶ Soils and topography are suitable for construction.
The standard does not apply to the handling or storage of fuels or to commercial or multilandowner agrichemical handling operations.

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Conservation Practice: Anaerobic Digester (Code 366)

Application: Production Area
An anaerobic digester is a component of a waste management system that provides
biological treatment in the absence of oxygen. Anaerobic digesters are designed to treat
manure and other by-products of animal agricultural operations for one or more of the
following reasons:
▶ To capture biogas for energy production.
▶ To manage odors.
▶ To reduce the net effect of greenhouse gas emissions.
▶ To reduce pathogens.
The practice applies where
▶ Biogas production and capture are components of a planned animal waste and
by‑product(s) management system.
▶ Sufficient and suitable organic feedstocks are readily available.
▶ Existing facilities can be modified to the requirements of this standard or for new
construction.
▶ The operator has the interest and skills to monitor and maintain processes or contracts
with a consultant to provide the services.

Conservation Practice: Animal Mortality Facility (Code 316)

Application: Production Area
Animal mortality facilities treat and dispose of livestock and poultry carcasses for routine
or catastrophic mortality events. Such facilities reduce effects on surface and groundwater
resources, reduce odors, and decrease the spread of pathogens. The planning and design
of animal mortality facilities or processes must conform to all federal, state, and local laws,
rules, and regulations.
This conservation practice applies to livestock and poultry operations where animal
carcass treatment or disposal is needed. This practice, however, might not be applicable to
catastrophic mortality resulting from disease, unless directed by the appropriate state or
federal authority (the state veterinarian or USDA APHIS).

Conservation Practice: Composting Facility (Code 317)

Application: Production Area
A composting facility is a structure or device to contain and facilitate the controlled aerobic
decomposition of manure or other organic material by microorganisms into a biologically
stable organic material that is suitable for use as a soil amendment.

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The purpose of this practice is to reduce the pollution potential and improve the handling
characteristics of organic waste solids. Composting facilities can also be used to produce a
soil amendment that adds organic matter and beneficial organisms, provides slow-release
plant-available nutrients, and improves soil condition.
This application applies where
▶ Organic waste material is generated by agricultural production or processing.
▶ The facility is a component of a planned waste management system.
▶ The facility can be constructed, operated, and maintained without polluting air or
water resources.
▶ The compost can be applied to the land or marketed to the public.

Conservation Practice:

Application:

Conservation Buffers
Contour Buffer Strips – (Code 332)
Contour Stripcropping – (Code 585)
Filter Strip – (Code 393)
Grassed Waterways – (Code 412)
Riparian Forest Buffer – (Code 391)
Stripcropping – (Code 586)
Terrace – (Code 600)
Windbreak – (Code 380)
Land-Application Areas/Production Area

All the conservation practices identified in the USDA CNMP Technical Guidance are
considered together because they all function to intercept sediment and other pollutants
to prevent them from reaching surface waters. Buffers function by intercepting runoff
containing nutrients, sediments and other potential pollutants; storing the runoff; and then
releasing it slowly into the waterbody. Buffers also reduce and contain flooding by slowing
water discharge into streams and providing an area for surplus water. Windbreaks also can
be used to reduce wind erosion and the deposition of soil into surface water. Some of the
conservation buffers can be applied in the land-application areas and to the production
area. Those practices include filter strips, contour buffer strips, and grassed waterways. The
use of such conservation practices around the production area would likely be limited to
those instances where surface water is near the production area.
Contour Buffer Strips: Contour buffer strips are strips of perennial vegetation, such as
grass, alternated with wider cultivated strips that are farmed on the contour. Contour
buffer strips allow runoff and trap sediment. Because the grass buffer strip is established on
the contour, runoff flows evenly across the entire surface of the strip, reducing sheet and rill
erosion. The grass slows runoff, helping the water soak into the soil and reducing erosion.
Sediment, nutrients and other pollutants are filtered from the runoff as it flows through the
strip thereby improving surface water quality. Buffer strips should be at least 15 feet wide
and usually make up one-fifth to one-third of the slope. The specific recommendations

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for establishing buffers vary from site to site. Cultivated strip widths are determined by
variables such as slope, soil type, field conditions, climate, and erosion potential. Contour
buffer strips are unsuitable in fields where irregular, rolling topography makes following a
contour impractical.
Contour Stripcropping: In stripcropping, crops are arranged so that a strip of grass or
forage is alternated with a strip of row crop (such as corn). The crops are planted across the
slope of the land, as in contour buffer strips. Less than half the field should be planted in
row crops. The grass or forage strips reduce erosion, slow runoff water, and trap sediment.
The practice combines the benefits of contouring and crop rotation. Strip cropping is not
as effective if the crop strips are too wide, especially on steep slopes. Maximum crop strip
widths range from 130 feet, for 1 to 2 percent slopes down, to 50 feet for 21 to 25 percent
slopes.
Grassed Waterways: Grassed waterways are natural or constructed vegetated channels
designed to direct surface water, flowing at non-erosive velocities, to a stable outlet (another
vegetated channel, earth ditch, or the like). Grassed waterways usually are used to control
gully erosion. In concentrated flow areas, grassed waterways can act as an important
component of erosion control by slowing the flow of water and filtering sediment. Other
benefits of grassed waterways include the safe disposal of runoff water, improved water
quality, improved wildlife habitat, reduced damage associated with sediment, and an
improvement in overall landscape aesthetics. Grassed waterways are typically used to
control runoff in a field. There might be circumstances, however, where they are used to
control runoff from the production area of an operation. Grassed waterways are usually
planted with perennial grasses, preferably native species where possible. Some common
grass species used in waterways are timothy, tall fescue, and Kentucky bluegrass. Grassed
waterways are generally constructed to be either trapezoid or parabolic in cross section,
with the requirement that the bottom (shorter) width of trapezoidal waterways not exceed
100 feet unless multiple or divided waterways are provided to control the meandering of
low flows.
Filter strips: Filter strips are areas of grass or other permanent vegetation that intercept
runoff, trapping sediment and pesticides before they reach a body of water. A properly
installed buffer can effectively trap 90 percent of sediment and nitrate moving from a farm
field. A filter strip can be 20 to 120 feet wide and is usually planted with native grasses.
Filter strips are one type of conservation buffer that is often applied to the area between the
production area and an adjacent waterbody. In those areas, a filter strip is a gently sloping
grass area that is planted between the livestock yard and drainage ways to streams and is
managed to filter runoff from the livestock yard. Influent waste is distributed uniformly
across the high end of the strip and allowed to flow through the strip. Nutrients and
suspended material remaining in the runoff water are filtered through the grass, absorbed
by the soil, and ultimately taken up by the plants. Filter strips should be designed and sized
to match the characteristics of the livestock yard. A typical practice is to make the filter
strip area about equal to the livestock yard area.

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Riparian Buffers: Riparian buffers are streamside vegetation consisting of trees, shrubs,
and grasses. They are used to intercept pollutants from an adjacent farm field. Riparian
buffers provide many important benefits by reducing the amounts of both eroded soil
sediment and nonpoint source pollutants (such as pesticides, herbicides, and surplus
nutrients) that enter surface water.
Terraces: Although terraces are not true buffer strips, they are linear conservation
practices that perform similar functions (e.g., water diversion, sediment trapping). They are
more commonly installed as a diversion measure. A diversion is an earthen embankment,
channel, or combination ridge and channel that is built across a slope to intercept and
store water runoff. Pollutants in terraces can leach into groundwater. Some terraces are
built level from end to end to contain water used to grow crops and recharge groundwater.
Others, known as gradient terraces, are built with some slope or grade from one end to the
other and can slow water runoff. Both help to reduce soil erosion. In the production area,
terraces can be used as a part of an overall diversion system based on the topography of
the feedlot. An earthen ridge or terrace can be constructed across the slope upgrade from a
production area to prevent runoff from entering the area or to direct runoff from one area of
the yard to a common collection area.
Windbreaks: The main purpose of windbreaks is to reduce wind erosion of soil from
agricultural fields and to protect farmsteads from severe wind. Windbreaks redirect
the wind and modify its force. They also provide habitat, food, and migration corridors
for wildlife; aesthetic benefits; livestock protection; and energy conservation. (Adapted
from NRCS’s National Handbook of Conservation Practices, at http://www.nrcs.usda.gov/
technical/standards/nhcp.html.)

Conservation Practice: Conservation Crop Rotation (Code 328)

Application: Land-Application Area
Crop rotation combined with recommended tillage practices can play an important role
in reducing wind and water erosion. Solid-seed crops such as small grains provide more
protection against water erosion than row crops, and permanent crops like hay or pasture
provide even more protection. Managing crops to provide sufficient residue throughout the
year is essential for satisfactory control of both wind and water erosion.
No-till or minimum-till farming is highly desirable as a conservation practice, but crop
rotation must be used to reduce the buildup of insects, weeds and disease-causing
organisms. Crop rotation also means that succeeding crops are of a genus, species,
subspecies, or variety different from that of the previous crop. Examples are barley after
wheat, row crops after small grains, and grain crops after legumes. The planned rotation
sequence could be for a 2- or 3-year period or longer. Legumes in the rotation can be
used to increase the available soil nitrogen. Symbiotic nitrogen-fixing bacteria called
Rhizobia form nodules on the roots of leguminous plants and fix atmospheric nitrogen or
convert it to organic nitrogen. The amount of nitrogen fixed varies with species, available
soil nitrogen, and many other factors. Fixed nitrogen not removed from the land by
harvest becomes available to succeeding crops as the legume tissues undergo microbial

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NPDES Permit Writers’ Manual for CAFOs

decomposition. A well-planned rotation can contribute to more efficient use of plant
nutrients. In a 3-year corn/alfalfa rotation, for example, manure can be applied during the
corn rotation, resulting in efficient use of nitrogen and often a buildup phosphorus and
potassium levels. During the alfalfa phase of the rotation, when manure is not applied,
the forage crop uses the soil phosphorus and potassium that were built up during the corn
phase of the rotation. The combination of nutrient management and crop rotation can
reduce or eliminate the need for purchased fertilizer. If conservation cropping is used in
the plan, the inspector should check that the sequence and types of crops being grown
are consistent with the plan. The nutrient application rates identified in the plan are based
on the specific crop rotation used in the calculations. (Adapted from NRCS National
Handbook of Conservation Practices, at http://www.nrcs.usda.gov/technical/standards/
nhcp.html.)

Conservation Practice: Cover Crop (Code 340)

Application: Land-Application Areas
A cover crop is a close-growing crop that temporarily protects the ground from wind and
water erosion during times when cropland is not adequately protected against soil erosion.
Common cover crops include cereal rye, oats, clover, crown vetch, and winter wheat. Cover
crops are most often recommended when low residue-producing crops such as soybeans or
corn silage are grown on erodible land. Note that if the cover crop is a legume, the nutrient
budget calculated in the operation’s NMP should account for the addition of nitrogen
provided by the crop to the soil.

Conservation Practice: Critical Area Planting (Code 342)

Application: Production Area
The USDA standard is for establishing permanent vegetation on sites that have or are
expected to have high erosion rates and on sites that have physical, chemical, or biological
conditions that prevent the establishment of vegetation with normal practices.
The purpose of this practice is to
▶ Stabilize areas with existing or expected high rates of soil erosion by water.
▶ Stabilize areas with existing or expected high rates of soil erosion by wind.
▶ Rehabilitate and revegetate degraded sites that cannot be stabilized through normal
farming practices.
▶ Stabilize coastal areas, such as sand dunes and riparian areas.
If gullies or deep rills are present, they will be treated, if feasible, to allow equipment
operation and ensure proper site and seedbed preparation. On the basis of a soil test, soil
amendments will be added, as necessary, to ameliorate or eliminate physical or chemical
conditions that inhibit plant establishment and growth. Required amendments should be

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NPDES Permit Writers’ Manual for CAFOs

included in the site specification with amounts, timing, and method of application. Such
required amendments include
▶ Compost or manure to add organic matter and improve soil structure and water
holding capacity.
▶ Agricultural limestone to increase the pH of acid soils.
▶ Elemental sulfur to lower the pH of calcareous soils.

Conservation Practice: Diversion (Code 362)

Application: Production Area
A diversion is an earthen channel with a supporting ridge constructed across a slope to
collect runoff water and safely divert it to a stable outlet, thereby preventing erosion of
an area below. Diversions are effective in intercepting storm runoff and directing it away
from fields susceptible to erosion, preventing water from flowing over areas where high
concentrations of pollutants are present (such as feedlots), and diverting runoff water away
from gullies to a stable outlet. The practice can also be applied in land-application areas to
reduce nutrient loss.
Diversions can be used to move surface water away from the production area to a cleanwater drainage system independent of the water-handling system. Such an approach
reduces the amount of water to be handled, reduces the amount of solids eroded from the
lot, and maintains available common diversion practices:
▶ Waterways, small terraces, and roof gutters to direct water away from the production
area.
▶ An earthen ridge or diversion terrace constructed across the slope to prevent runoff
from entering the production area.
▶ A catch basin with a pipe outlet installed above the production area if a diversion
terrace is not practical.
All roofs that would contribute to runoff from the production area should have gutters,
downspouts, and outlets that discharge water away from the confinement area. The design
of the diversion should be based on a 25 year, 24-hour storm.

Conservation Practice: Fence (Code 382)

Application: Production Area/Land-Application Area
An area of land can be enclosed or divided with a suitable permanent structure that acts as
a barrier to livestock.

Conservation Practice: Field Border (Code 386)

Application: Land-Application Areas
The USDA standard defines a field border as a strip of permanent vegetation established at
the edge or around the perimeter of a field.

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The practice can be applied to accomplish one or more of the following:
▶ Reduce erosion from wind and water.
▶ Protect soil and water quality.
▶ Manage pest populations.
▶ Provide wildlife food and cover.
▶ Increase carbon storage.
▶ Improve air quality.
The practice is applied around the perimeter of fields. Its use can support or connect other
buffer practices within and between fields. The practice can also apply to recreation land or
other land uses where agronomic crops including where forages are grown.

Conservation Practice: Heavy-Use Area Protection (Code 561)

Application: Production Area
The USDA standard establishes the stabilization of areas frequently and intensively used by
people, animals, or vehicles by any combination of establishing vegetative cover, surfacing
with suitable materials, or installing needed structures.
The purpose of the practice is to provide a stable, non-eroding surface for areas frequently
used by animals, people or vehicles. It also helps to protect and improve water quality.
The treated area can include all areas where livestock congregate and cause surface
stability problems. That includes feeding areas, portable hay rings, watering facilities,
feeding troughs, mineral boxes, and other facilities where livestock concentrations cause
resource concerns.
To reduce the negative water quality impact of heavy-use areas, consider locating them as
far as possible from waterbodies or water courses. In some cases, it could require relocating
the heavily used area rather than armoring an area that is already in use.

Conservation Practice: Irrigation Water Management (Code 449)

Application: Land-Application Area
Irrigation water management is controlling the rate, amount, and timing of irrigation water
in a planned and prudent manner. The purpose of the practice is to manage soil moisture
for crop production and erosion control, minimize leaching of soluble plant nutrients, and
protect groundwater and surface water quality. Without proper management, fields are
often irrigated too often and at excessive rates. If irrigation water is over-applied, the excess
water can cause soil erosion and leaching of nutrients and pesticides. Over-application
also wastes water, energy, and money. The volume of water applied and the frequency of
applications should determined by crop needs and soil conditions. Soil moisture should
be monitored to predict when irrigation is needed. When crops are irrigated, the volume
applied should not exceed the available water-holding capacity of the soil in the root zone

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NPDES Permit Writers’ Manual for CAFOs

or the moisture control zone. In addition, the infiltration rate of the soil should not be
exceeded. This practice should be applied in conjunction with other erosion and sediment
control practices. (Adapted from NRCS’s National Handbook of Conservation Practices, at
http://www.nrcs.usda.gov/technical/standards/nhcp.html.)

Conservation Practice: Livestock Shade Structure (Code 717)

Application: Pasture
This standard is available in some states but is not included in the National Handbook of
Conservation Practices. The standard describes a livestock shade structure as a portable,
metal frame structure with a mesh fabric roof that is to provide shade for livestock. The
practice can be applied as part of a resource management system to protect livestock from
excessive heat and also to protect surface waters from pollution by excluding livestock
from existing shade on streambanks. The standard includes considerations for the design,
placement, construction, operation, and maintenance of livestock shade structures.

Conservation Practice: Nutrient Management (Code 590)

Application: Land Application
The USDA CNMP Technical Guidance uses NRCS Conservation Practice Standard 590,
Nutrient Management, to guide the proper land application of nutrients. The standard
states that nutrient application rates are to be established considering current soil tests,
realistic yield goals and management capabilities. In cases where manure is the source of
applied nutrients, the rate also shall be based on an analysis of the nutrient value of the
manure, NRCS book values, or historical documented records.

Conservation Practice:

Application:

Residue Management (Code 344)
No-Till and Strip Till (Code 329A)
Mulch Till (Code 345)
Ridge Till (Code 346)
Land Application

These cropping practices retain crop residues on or near the surface of a field. As a group
these practices are often referred to as conservation tillage. Conservation tillage is any
tillage system that leaves at least 30 percent of the field surface covered with crop residue
after cropping is completed, and it involves reduced or minimum tillage. The residue
can reduce soil detachment by absorbing the impact of falling raindrops. The remaining
residue might form small dams that can retard runoff and create puddles of water that
absorb raindrop energy, thus reducing soil erosion. Such practices require use of some
specialized equipment.
No-till/strip till: In these systems, the soil is left undisturbed from harvest to planting
except for strips up to one-third of the row width. (The strips could involve only residue
disturbance or could include soil disturbance.) Planting or drilling is accomplished using
disc openers, coulter(s), row cleaners, in-row chisels, or rototillers. Weeds are controlled

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primarily with crop protection products; cultivation can be used for emergency weed
control. Other common terms used to describe no-till, include row-till, and slot-till.
Ridge-till: Ridge-till is a system in which seeds are planted into a seedbed prepared
by scraping off the top of the ridge. The scraped-off ridge usually provides an excellent
environment for planting. Ridges are formed during cultivation of the previous year’s crop.
Ridge-till operations consist of planting in the spring and at least one cultivation to recreate
the ridges for the next year. Rows remain in the same place each year and any crop residue
on the ridges at planting is pushed between the rows.
Mulch-till: This system uses full-width tillage involving one or more tillage strips, which
disturbs the entire soil surface and is done before or during planting. Tillage tools such as
chisels, field cultivators, discs, sweeps, or blades are used. Weeds are controlled with crop
protection products or cultivation or both.

Conversation Practice: Roof Runoff Management (Code 558)

Application Area: Production Area
This USDA Conservation Practice Standard is not identified in the CNMP Technical
Guidance; however, it can be used to address roof runoff entering the production area.
This USDA standard establishes the plans and specifications for designing, constructing,
and operating roof runoff management facilities. Such facilities include erosion-resistant
channels or subsurface drains with rock-filled trenches along building foundations below
eaves, roof gutters, downspouts, and appurtenances.
The purpose of this practice is to prevent roof runoff water from flowing across
concentrated waste areas, barnyards, roads and alleys; reduce pollution and erosion;
improve water quality; prevent flooding; improve drainage; and protect the environment.

Conversation Practice: Roofs and Covers (Code 367)

Application Area: Production Area
The practice standard addresses a rigid, semi-rigid, or flexible manufactured membrane,
composite material, or roof structure placed over a waste management facility to provide a
roof or cover for
▶ Improving water quality.
▶ Diverting clean water from animal management areas (i.e., barnyard, feedlot or
exercise area) or waste storage facilities.
▶ Capturing biogas for energy production.
▶ Reducing net effect of greenhouse gas emissions.
▶ Improving air quality and reducing odor.
The practice criteria address the structure’s service life, materials, loads, design, access,
repair, and safety. Operation and maintenance requirements are included.

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Conservation Practice: Sediment Basin (Code 350)

Application: Production Area/Land-Application Area
The USDA standard defines this practice as a basin constructed with an engineering outlet,
formed by an embankment or excavation or a combination of the two.
The purpose of the practice is to capture and detain sediment laden runoff, or other debris,
for a sufficient length of time to allow it to settle out in the basin.
This practice applies to urban land, construction sites, agricultural land, and other
disturbed lands where
▶ Physical conditions or land ownership precludes treatment of a sediment source by
installing erosion-control measures.
▶ A sediment basin offers the most practical solution.
▶ Failure of the basin will not result in loss of life, damage to homes, commercial or
industrial buildings, main highways or railroads, or in the use of public utilities.
▶ The product of the storage times the effective height of the dam is less than 3,000.
Storage is the volume, in acre-feet, in the reservoir below the elevation of the crest of
the auxiliary spillway.
▶ The effective height of the dam is 35 feet or less. The effective height of the dam is the
difference in elevation, in feet, between the auxiliary spillway crest and the lowest
point in the cross section taken along the centerline of the dam.
▶ The Hazard Class of the dam is low.

Conservation Practice: Solid/Liquid Waste Separation Facility (Code 632)

Application: Production Area
A solid/liquid waste separation facility is a filtration or screening device, settling tank,
settling basin, or settling channel used to separate a portion of solids from a liquid waste
stream.
The practice is used to partition solids, liquids and their associated nutrients as part of a
conservation management system to improve or protect air and water quality and animal
health, or to meet other management objectives.
This practice applies where solid/liquid separation will
▶ Remove solids from the liquid waste stream as a primary treatment process and allow
further treatment processes to be applied such as composting and anaerobic digestion.
▶ Allow partly digested feed to be separated from the liquid waste stream so that it can
be used as a feed supplement or for bedding.
▶ Reduce problems associated with solids accumulation in liquid storage facilities.

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NPDES Permit Writers’ Manual for CAFOs

▶ Reduce solids in stored liquids so liquids can be recycled for other uses (i.e. flush
water).
▶ Reduce solids in stored liquids to better facilitate land application of liquids using
irrigation techniques.
▶ Assist with partitioning nutrients in the waste stream to improve nutrient
management.

Conservation Practice: Structure for Water Control (Code 587)

Application: Production Area
The USDA standard establishes a structure in a water management system that conveys
water, controls the direction or rate of flow, maintains a desired water surface elevation, or
measures water.
The practice can be applied as a management component of a water management system to
control the stage, discharge, distribution, delivery, or direction of water flow.
The practice applies wherever a permanent structure is needed as an integral part of a
water-control system to serve one or more of the following functions:
▶ Convey water from one elevation to a lower elevation within, to, or from a water
conveyance system such as a ditch, channel, canal, or pipeline designed to operate
under open channel conditions. Typical structures are drops, chutes, turnouts, surface
water inlets, head gates, pump boxes, and stilling basins.
▶ Control the elevation of water in drainage or irrigation ditches. Typical structures are
checks, flashboard risers, and check dams.
▶ Control the division or measurement of irrigation water. Typical structures are division
boxes and water measurement devices.
▶ Keep trash, debris or weed seeds from entering pipelines. A typical structure is a debris
screen.
▶ Control the direction of channel flow resulting from tides and high water or back-flow
from flooding. Typical structures are tide and water management gates.
▶ Control the water table level, remove surface or subsurface water from adjoining land,
flood land for frost protection, or manage water levels for wildlife or recreation. Typical
structures are water level control structures, flashboard risers, pipe drop inlets, and
box inlets.
▶ Convey water over, under, or along a ditch, canal, road, railroad, or other barriers.
Typical structures are bridges, culverts, flumes, invented siphons, and long span pipes.
▶ Modify water flow to provide habitat for fish, wildlife, and other aquatic animals.
Typical structures are chutes, cold water release structures, and flashboard risers.
▶ Provide silt management in ditches or canals. A typical structure is a sluice.

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NPDES Permit Writers’ Manual for CAFOs

▶ Supplement a resource management system on land where organic waste or
commercial fertilizer is applied.
▶ Create, restore, or enhance wetland hydrology.

Conservation Practice: Waste Storage Facility (Code 313)

Application: Production Area/Land-Application Area
The USDA standard defines this practice as a waste storage impoundment made by
constructing an embankment or excavating a pit or dugout, or by fabricating a structure.
The purpose of the standard is to temporarily store wastes such as manure, wastewater,
and contaminated runoff as a storage function component of an agricultural waste
management system.
Conditions where this practice applies include
▶ Where the storage facility is a component of a planned agricultural waste management
system.
▶ Where temporary storage is needed for organic wastes generated by agricultural
production or processing.
▶ Where the storage facility can be constructed, operated, and maintained without
polluting air or water resources.
▶ Where site conditions are suitable for constructing the facility.
▶ Facilities using embankments with an effective height of 35 feet or less where damage
resulting from failure would be limited to damage of farm buildings, agricultural land,
or township and county roads.
▶ Where fabricating structures including tanks, stacking facilities, and pond
appurtenances.

Conservation Practice: Waste Treatment Lagoon (Code 359)

Application: Production Area
A waste treatment lagoon is an impoundment made by constructing an embankment or
excavating a pit or dugout.
The purpose of the practice is to biologically treat waste, such as manure and wastewater,
and thereby reduce pollution potential by serving as a treatment component of a waste
management system.
Lagoons should be outside floodplains to minimize the potential for stream contamination
and should have as little drainage area as possible.
The practice can be applied under the following conditions:
▶ The lagoon is a component of a planned agricultural waste management system.

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NPDES Permit Writers’ Manual for CAFOs

▶ Treatment is needed for organic wastes generated by agricultural production or
processing.
▶ On any site where the lagoon can be constructed, operated, and maintained without
polluting air or water resources.
▶ At lagoons using embankments with an effective height of 35 feet or less, where
damage resulting from failure would be limited to damage of farm buildings,
agricultural land, or township and country roads.

Conservation Practice: Waste Utilization (Code 633)

Application: Land-Application Areas
This practice applies where agricultural wastes that include animal manure and
wastewater from livestock and poultry operations are generated or used. The standard
recommends sampling and analysis requirements for the manure and wastewater as well
as record-keeping requirements. In addition to general criteria, the standard includes
specific criteria to protect water quality.
All agricultural waste shall be utilized in a manner that minimizes the opportunity
for contaminating surface and groundwater supplies. Agricultural waste shall not be
applied on soils that are frequently flooded, as defined by the National Cooperative Soil
Survey, during the period when flooding is expected. When liquid wastes are applied, the
application rate must not exceed the infiltration rate of the soil, and the amount of waste
applied must not exceed the moisture-holding capacity of the soil profile at the time of
application.
The standard also includes criteria to reduce atmospheric losses and the reduction of odors
from spreading operations. (Adapted from NRCS’s National Handbook of Conservation
Practices, at http://www.nrcs.usda.gov/technical/standards/nhcp.html.)

Conservation Practice: Water and Sediment Control Basin (Code 638)

Application: Production Area/Land-Application Area
The USDA standard defines the practice as an earth embankment or a combination ridge
and channel constructed across the slope of minor watercourses to form a sediment trap
and water detention basin with a stable outlet.
The practice can be applied as part of a resource management system for one or more of the
following purposes:
▶ To reduce watercourse and gully erosion.
▶ To trap sediment.
▶ To reduce and manage onsite and downstream runoff.
This practice applies to sites where
▶ The topography is generally irregular.

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NPDES Permit Writers’ Manual for CAFOs

▶ Watercourse or gully erosion is a problem.
▶ Sheet and rill erosion is controlled by other conservation practices.
▶ Runoff and sediment damages land and works of improvements.
▶ Adequate outlets can be provided.
Do not use this standard in place of terraces. When the ridge or channel extends beyond
the detention basin or level embankment, use Conservation Practice Standard (600),
Terrace or (362) Diversion, where appropriate.

Appendix K: NRCS Conservation Practice Standards

NPDES Permit Writers’ Manual for CAFOs

Appendix
Nutrient Management
Planning Software

L

NPDES Permit Writers’ Manual for CAFOs

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Software Programs
This appendix describes the types of software available to develop nutrient management plans
(NMPs) and which programs are used in specific states. Permit writers should be familiar with
the program(s) commonly used in their state to ensure they are familiar with the format and
content of NMPs they will be reviewing. Table L-1 below describes which software is being used
in each state, and Table L-2 provides a brief description of each software program along with
contacts and websites to refer to for more information. EPA has supported the development of
Manure Management Planner (MMP), and this appendix briefly outlines how MMP works and
who can and should use it.
Table L-1. Specific software programs available in each state

State
Alabama

NMP software available

Description
number in
Table 2

Manure Management Planner (MMP)

4

MMP

4

California Central Valley NMP

1

MMP

4

MMP

4

Alaska
Arizona
Arkansas
California
Colorado
Connecticut
Delaware

NuMan MD Pro 3.0

10

MMP

4

Florida

MMP

4

Georgia

MMP

4

Idaho

Idaho OnePlan

3

Illinois

MMP

4

Indiana

MMP

4

Iowa

MMP

4

Hawaii

Kansas
Kentucky

Nutrient Utilization Plan Worksheet

13

MMP

4

MMP

4

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Table L-1. Specific software programs available in each state (continued)

State

NMP software available

Description
number in
Table 2

Louisiana
Maine

Maryland

NuMan MD Pro 3.0

10

NuMan Reporter 2.0

12

MMP

4

Massachusetts

MMP

4

Michigan

MMP

4

MPCA MMP

5

Minnesota

NMP for Minnesota

11

MMP

4

Mississippi

MMP

5

Missouri

MMP

5

Montana

MMP

5

Nebraska

MMP

5

MMP

5

NMSU Soil Test Interpretation Report Software

7

NMSU Dairy Annual Nutrient Manager Software

6

MMP

4

Cropware

2

North Carolina Nutrient Management Software

8

MMP

4

Nevada
New Hampshire
New Jersey

New Mexico

New York
North Carolina
North Dakota
Ohio
Oklahoma

Crop Nutrient Management Software

14

MMP

4

MMP

4

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Table L-1. Specific software programs available in each state (continued)

State
Oregon

Pennsylvania

Description
number in
Table 2

NMP software available
Oregon OnePlan

15

MMP

4

Penn State NMP Spreadsheet

16

MMP

4

MMP

4

NRCS Tool in South Dakota

9

MMP

4

Tennessee

MMP

4

Texas

Texas Waste Utilization and Nutrient Management Plan
Worksheet

18

Utah’s Manure Actual Nutrient Content spreadsheet

19

Puerto Rico
Rhode Island
South Carolina
South Dakota

Utah
Vermont

MMP

4

MMP

4

Virgin Islands
Virginia

NuMan Reporter 2.0

Washington

MMP

West Virginia

NuMan Reporter 2.0

12

SNAP Plus

17

Wisconsin

MMP

12
4

4

Wyoming

Appendix L: Nutrient Management Planning Software

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Table L-2. Description of software programs
Number
1

2

3

Software

Description

For more information

California
Central Valley
Dairy Waste
and Nutrient
Management
Software

Designed for existing milk cow dairies
as mandated by the Waste Discharge
Requirements General Order No.
R5-2007-0035. The software is applicable
to owners and operators of existing milk
cow diaries that were operating as of
October 17, 2005, filed a complete Report
of Waste Discharge in response to the 2005
Report of Waste Discharge Request Letter,
and have not expanded since October 17,
2005. The software was developed with
a grant from the California State Water
Resources Control Board and was designed
to minimize leaching of nutrients and salts
to groundwater and transport of those
constituents to surface water.

See the California EPA website.
Adobe PDF Reader software is
needed.

Cropware

Supported by the NYS NRCS, the NYS
Department of Agriculture and Markets,
and the NYS Department of Environmental
Conservation. It is a key component of
Comprehensive NMPs (CNMPs) as it can
develop plans in accordance with the NRCS
Nutrient Management Standard (Standard
590). For effective nutrient management
planning, Cropware integrates Cornell
crop nutrient guidelines for a full range of
agronomic and vegetable crops, nutrient
credits from various sources including
manure, soil, sod, and fertilizer, and
environmental risk indices, including the
New York State Phosphorus Runoff Index and
the Nitrate Leaching Index.

Cropware Version 2.0.34
operates on Microsoft
Windows operating systems
and is available to any New
York user at no charge. For
a Cropware training session,
questions about the software,
or to order a Cropware CD,
contact Patty Ristow at
plr27@cornell.edu

Combines government regulations and
current best management practices (BMPs)
for agriculture into a single plan. This
software is designed to include nutrient, pest
and waste management, water quality and
wetlands, air quality, financial assistance,
endangered species, and petroleum storage
tanks.

Information on how to become
certified to use the Nutrient
Management Planner is at
http://oneplan.org/NMPlan.asp

Idaho OnePlan

The OnePlan software questionnaire along
with data access to aerial photos, soil data,
hydrology maps, roads, and GIS maps is used
to generate a report and plan of action with
effective area-specific BMPs.

Appendix L: Nutrient Management Planning Software

http://www.waterboards.ca.gov/
centralvalley/water_issues/
dairies/complying_with_general_
order/software/index.shtml

http://nmsp.cals.cornell.edu/
software/cropware.html

For information regarding
NMP software training, contact
Hillary Simpson, State Nutrient
Management Coordinator at
the Idaho State Department of
Agriculture at (208) 736-3049
or hsimpson@agri.idaho.gov

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Table L-2. Description of software programs (continued)
Number

Software

Description

3

Idaho OnePlan
(continued)

The Idaho OnePlan Nutrient Management
Planner is the only officially recognized
planning tool for creating certified NMPs in
Idaho. The software and training to become
Certified Nutrient Management Planners in
Idaho is offered by the state and the USDA.

4

Manure
Management
Planner (MMP)

See the description below.

For more information

http://www.agry.purdue.edu/
mmp/
For agronomic questions,
contact Brad Joern
at (765) 494-9767 or
bjoern@purdue.edu
For software questions, contact
Phil Hess at (765) 494-8050 or
pjhess@purdue.edu

5

6

7

MPCA Manure
Management
Planner

Developed by the Minnesota Pollution
Control Agency (MPCA), the MMP is
a spreadsheet that is designed to meet
Minnesota 7020 feedlot rule requirements.
This MMP is required for operations with
100 or more animal units (AU) after October
23, 2000, or when manure from a feedlot
capable of holding 300 or more AU is applied
by someone other than a certified animal
waste technician. Because records of actual
manure application practices are required
at all facilities with 100 or more AU, this
program also has a record-keeping tab.

www.pca.state.mn.us/hot/
feedlot-management.html

NMSU Dairy
Annual Nutrient
Manager
Software

Developed by New Mexico State University
and USDA, it balances nutrients according
to user-defined crops planted, soil analyses,
effluent irrigated, dry manure applied, and
chemical fertilizers used.

http://aces.nmsu.edu/ces/dairy/
tools.html

NMSU Soil Test
Interpretation
Report Software

Microsoft Excel spreadsheet developed by
New Mexico State University and NRCS to
recommend nutrient application for crop
production. This software is a requirement
for both organic manure applications and
inorganic fertilizer applications to apply
the 590 Nutrient Management practice.
This software requires soil values including
salinity, pH, phosphorous, and potassium
obtained from proper soil testing.

http://www.nm.nrcs.usda.gov/
technical/water/nmafo.html

George Schwint, MPCA
Feedlot Engineer, at
(303) 214-3793 or
George.schwint@pca.state.mn.us

Victor E. Cabrera, Extension
Dairy Specialist,
at (505) 985-2292 x107 or at
vcabrera@nmsu.edu

Appendix L: Nutrient Management Planning Software

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NPDES Permit Writers’ Manual for CAFOs

Table L-2. Description of software programs (continued)
Number
8

9

10

11

Software

Description

For more information

North Carolina
Nutrient
Management
Software

The North Carolina Nutrient Management
Software is useful in writing commercial
fertilizer and animal waste plans. It produces
NMPs in the required format to meet state
requirements for Waste Management Plans
for animal operations.

Can be downloaded at http://
www.soil.ncsu.edu/programs/
nmp/ncnmwg/nmp/software.htm

NRCS Tool in
South Dakota

South Dakota uses the NRCS Tool for
developing an initial NMP, the NRCS Tool
for annual NMP using the phosphorus
assessment tool, and the DENR Tool for
calculating manure application rates.

http://denr.sd.gov/des/sw/
ManureNutrientManagement
Tools.aspx

Nutrient
Management
for Maryland
Version 3.0
(NuMan
Pro 3.0)

NuMan Pro 3.0 is the most advanced
Windows software available to complete
Maryland NMPs. It is derived from the
NuMan Reporter 2.0.

http://www.anmp.umd.edu/
Software/index.cfm

Nutrient
Management
Planner for
Minnesota

Nutrient Management Planner Version
3.0 was developed by the University of
Minnesota Extension Service and the USDANRCS. This planning aid will produce an
MMP to meet MPCA requirements for
most feedlots and NRCS requirements. It is
designed to assist producers and agronomists
plan and keep records of field-specific
fertilizer and manure applications.

Requires Microsoft Access 2003
or Access 2007 and can be
ordered from the University of
Minnesota Extension at
http://shop.extension.umn.edu

Vernon Cox at
(919) 715-6109

Kent Woodmansey at
(605) 773-3351

Direct questions to
http://www.anmp.umd.edu/
About_NM/Staff.cfm

Ann Lewandowski at UM Water
Resources Center at
alewand@umn.edu or
(612) 624-6765.

Specifically, it can develop annual fieldspecific NMPs for crop and livestock farms,
create long-range strategic NMPs including
CNMPs, and provide crop recommendations.
The crop recommendations are consistent
with the USDA-NRCS-Minnesota 590
Standard for nutrient management and are
based on published information from the
University of Minnesota Extension Service.
12

Nutrient
Management
Reporter Version
2.0 (NuMan
Reporter 2.0)

NuMan Reporter 2.0 is a software program
designed to help prepare the Maryland
Department of Agriculture’s Annual
Implementation Report (AIR). The AIR
describes the nutrient management activities
that have been applied over the past year.
NuMan Reporter 2.0 is not required to
complete this report but facilitates the

Appendix L: Nutrient Management Planning Software

http://www.anmp.umd.edu/
Software/numanreporter_
features.cfm
Contact the Agricultural
Nutrient Management
Program at (301) 405-1318.

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Table L-2. Description of software programs (continued)
Number

Software

Description

For more information

12

Nutrient
Management
Reporter Version
2.0 (NuMan
Reporter 2.0)
(continued)

reporting process. NuMan Reporter 2.0
can also be used to generate other NMPs.
This program is designed to summarize the
number of acres, total amount of nutrients
recommended as fertilizer, and the total
amounts of organic material recommended
on a crop code basis.

13

Nutrient
Utilization Plan
Worksheet

Form with spreadsheets specific to swine
and non-swine facilities to calculate elements
required for the NMP.

http://www.kdheks.gov/feedlots/

14

Ohio Crop
Nutrient
Management
Software

The Crop Nutrient Management software
is a tool to help Ohio farmers develop a
manure NMP. After soil and manure testing is
performed to analyze nutrient availability, the
software is used to determine the appropriate
nutrient application for each field. The final
development of a manure NMP can be
done with the assistance of the local Soil
and Water Conservation District and the soil
conservationist.

http://ohioline.osu.edu/agffact/0207.html
For assistance, contact an Ohio
county Extension agent or
Soil and Water Conservation
District technician

The software was developed by the Ohio
State University Extension and is available at
Ohio county Extension offices for a nominal
charge.
15

16

Oregon
OnePlan

Penn State
Nutrient
Management
Plan
Spreadsheet

The Oregon OnePlan is nutrient
management software developed jointly
by the Idaho Department of Agriculture,
the NRCS, EPA, USDA Agricultural Research
Service, University of Idaho College of
Agriculture and Marshall and Associates.
The software is a modification of Idaho’s
OnePlan for use in Oregon. It is designed for
developing CNMPs and for preparing Field
Annual Nutrient Budgets.

At the time of publication, an
active link to Oregon OnePlan
was not available.

The Penn State Nutrient Management Plan
Spreadsheet is a tool designed to produce
the necessary components of an NMP
as required by Pennsylvania’s Nutrient
Management Act (Act 38, 2005) Program.

http://panutrientmgmt.cas.psu.
edu/main_planning_tools.htm

Jennifer Zwicke, NRCS Oregon
Environmental Engineer at
(503) 414-3231 or Jennifer.
Zwicke@or.usda.gov

Jennifer Weld, Project Associate
at Penn State University, at
(570) 366-1558 or
jlm23@psu.edu

Appendix L: Nutrient Management Planning Software

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Table L-2. Description of software programs (continued)
Number

Software

Description

For more information

SNAP-Plus
Nutrient
Management
Software

SNAP-Plus is a Microsoft Windows-based
program designed for preparing NMPs
in accordance with Wisconsin’s Nutrient
Management Standard Code 590. It is a
simple software program consisting of several
models including nutrient management
(SNAP), conservation assessment (RUSLE2),
and the Wisconsin Phosphorus Index (PI) that
is designed to make multiyear nutrient and
conservation planning easier.

http://www.snapplus.net/

18

Texas Waste
Utilization
and Nutrient
Management
Plan Worksheet

The Texas Waste Utilization and Nutrient
Management Plan Worksheet develops a
plan that will meet the USDA-NRCS Nutrient
Management (590) Standard and Waste
Utilization (633) Standard for all types of
livestock. The worksheet incorporates the
animal waste spreadsheet for liquids, solids,
biosolids, as well as both poultry-producer
and non-producer spreadsheets. It also
contains the Phosphorus Index spreadsheet
used in Texas.

http://nmp.tamu.edu/

19

Utah’s Manure
Actual Nutrient
Content
spreadsheet

No information found

17

Sue Porter at
(608) 224-4605 or
Sue.Porter@wisconsin.gov

Manure Management Planner (MMP)
The U.S. Environmental Protection Agency (EPA), in coordination with the U.S. Department
of Agriculture (USDA), has worked on developing a planning tool that would generate a single
document that meets the objectives of both agencies. The one document would include
the required elements of an NMP and the elements of a voluntary comprehensive nutrient
management plan (CNMP) developed in accordance with USDA technical guidance. A CNMP is
a plan much like the NMP required by EPA’s CAFO regulations. There are some minor differences
between the scope of the two documents, such as a CNMP option to include feed management
plans (which are not required for the NMP) and an NMP requirement to address chemical
disposal (which is not part of a CNMP). However, the EPA and USDA agree that there is no reason
why one document could not suffice for both the CNMP and NMP by accommodating both
agencies’ requirements. To that end, EPA and USDA have partnered to develop MMP, software
that integrates both sets of planning requirements. Even though both agencies promote the use
of a single tool, it remains the CAFO operator’s responsibility to provide that information to the
director to meet the requirements of the CAFO rule, because USDA does not make facility-specific
information available to other agencies or the public. EPA encourages the use of MMP to facilitate
the development and review of NMPs under the NPDES permit program.

Appendix L: Nutrient Management Planning Software

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NPDES Permit Writers’ Manual for CAFOs

The MMP software, developed under a grant from EPA and USDA to Purdue University, is a
computer program that provides permitting authorities and producers with a mix of programs,
not available elsewhere, to assist in CNMP and NMP development. The objective of the effort was
to accelerate the CNMP and NMP development process by integrating other software used to
calculate manure application rates. Among those tools are the revised universal soil loss equation
(RUSLE2), the Phosphorus Index (PI), and other state-specific risk assessment tools used in CNMP
and NMP development. MMP incorporates field-specific data tables that allow the producer
to list the type of crops planned, crop rotation by planting season, nutrients available for each
crop on the basis of previous manure applications and the rate of application per crop. MMP
helps the user allocate manure (where, when, and how much) on a monthly basis for the length
of the plan (1–10 years). That allocation process helps determine if the operation has sufficient
crop acreage, seasonal land availability, manure storage capacity, and application equipment to
manage the manure produced in an environmentally responsible manner. MMP is also useful for
identifying changes that may be needed for a non-sustainable operation to become sustainable
and determine what changes might be needed to keep an operation sustainable if the operation
expands. MMP’s data tables provide permitting authorities with specific information that can be
extracted as terms of the NMP to be inserted into a permit.
Version 0.3.0.1 (October 11, 2010) of MMP supports 34 states (Alabama, Arkansas, California,
Colorado, Delaware, Florida, Georgia, Iowa, Illinois, Indiana, Kansas, Kentucky, Massachusetts,
Maryland, Michigan, Minnesota, Missouri, Mississippi, Montana, North Dakota, Nebraska,
New Jersey, New Mexico, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, South
Dakota, Tennessee, Utah, Vermont, Washington, and Wisconsin) and generates fertilizer
recommendations based on each state’s extension guidelines. The MMP software is available
without charge. It is strictly a voluntary tool. There might be some situations at a livestock
operation, such as varying terrains and unusual cropping sequences, that MMP cannot
accommodate; thus the program might not be a good fit for all operators. Permitting authorities
and producers can still choose to use established state NMP software to develop and implement
their NMP. More information on MMP is at the Purdue University Web site, http://www.agry.
purdue.edu/mmp/.

Appendix L: Nutrient Management Planning Software

NPDES Permit Writers’ Manual for CAFOs

Appendix

M

Nutrient Management
Recordkeeping Calendar
Template
This calendar is adapted from the University of Nebraska Extension publication,
Nutrient Management Recordkeeping Calendar: July 2011–December 2012.
EPA thanks Nebraska Extension, Leslie Johnson, and Purdue University for permission
to adapt the calendar for use in the Permit Writers’ Manual.

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Appendix
References for NPDES
Permit Writers

N

NPDES Permit Writers’ Manual for CAFOs

N-1

NPDES Permit Writers’ Manual for CAFOs

EPA Programs and Information
NPDES Permit Program Basics
This website provides basic permitting tools and information.
http://cfpub.epa.gov/npdes/home.cfm?program_id=45
NPDES Permit Writers’ Manual
U.S. EPA NPDES Permit Writers Manual
EPA 833-­B-96-003, December 1, 1996.
To download individual chapters or the entire document, go to EPA’s NPDES Permit Writers’
Manual page at
http://cfpub.epa.gov/npdes/writermanual.cfm?program_id=45
CAFO Final Rule Web Page
This website provides access to the text of the rule and preamble, outreach brochures, supporting
documents, and guidance documents.
http://www.epa.gov/npdes/caforule
Enforcement & Compliance History Online (ECHO)
EPA website for online inspection, violation, and enforcement facility data on CAFOs from PCS or
ICIS.
http://www.epa-echo.gov/echo/compliance_report_water.html
TMDL Program
EPA Office of Wetlands, Oceans and Watersheds. TMDL Program
http://www.epa.gov/OWOW/tmdl/index.html
Clean Water Act Section 319 Nonpoint Source Management Program
EPA Office of Wetlands, Oceans and Watersheds, Clean Water Act Section 319
http://www.epa.gov/owow/nps/cwact.html
Source Water Protection Programs
EPA Office of Groundwater and Drinking Water, Source Water Protection
http://www.epa.gov/safewater/protect.html
Development Document for the Final Revisions to the National Pollutant Discharge
Elimination System (NPDES) Regulation and the Effluent Guidelines for Concentrated Animal
Feeding Operations
EPA-821-R-03-001
Chapter 4 of this document contains an overview of the livestock industry and profiles of specific
animal sectors that EPA compiled for the 2003 CAFO rule revisions.
http://www.epa.gov/npdes/pubs/cafo_dev_doc_p1.pdf

Appendix N: References for NPDES Permit Writers

N-2

NPDES Permit Writers’ Manual for CAFOs

National Management Measures to Control Nonpoint Source Pollution from Agriculture
EPA 841-B-03-004, 2003
Includes information on selecting and implementing BMPs to control the contribution of
pollutants to surface water.
http://www.epa.gov/owow/nps/agmm/index.html
Risk Assessment Evaluation for Concentrated Animal Feeding Operations
EPA/600/R-04/042, May 2004
This document discusses risk factors associated with CAFOs, including nutrients and pathogens.
http://nepis.epa.gov/Exe/ZyPURL.cgi?Dockey=901V0100.txt
Routine Biosecurity Procedures for EPA Personnel Visiting Farms, Ranches, Slaughterhouses
and Other Facilities with Livestock and Poultry
December 10, 2001
http://www.epa.gov/oecaerth/resources/policies/monitoring/inspection/biosecuritymemo.pdf
National Agriculture Compliance Assistance Center (Ag Center)
http://www.epa.gov/agriculture/agctr.html
Non-Water Quality Impact Estimates for Animal Feeding Operations
Eastern Research Group for USEPA, December 2002
Sections 304(b) and 306 of the CWA require that EPA consider non-water quality environmental
impacts of ELGs. This document provides an analysis of non-water quality impacts of the CAFO
ELGs, particularly air emissions and energy impacts.
http://www.epa.gov/npdes/pubs/cafo_nonwaterquality.pdf
Air Emissions from Animal Feeding Operations: Current Knowledge, Future Needs
National Academy of Sciences, February 2003
This document presents the findings of the ad hoc committee tasked by USEPA and USDA to
evaluate estimates of air emissions from animal feeding operations, identify research needs, and
recommend modeling methods.
http://www.epa.gov/ttn/chief/ap42/ch09/related/nrcanimalfeed_dec2002.pdf

USDA Programs and Information
2008 Farm Bill
USDA’s online gateway to information about the 2008 Farm Bill.
http://www.ers.usda.gov/FarmBill/2008/
USDA Natural Resources Conservation Service (NRCS)
http://www.nrcs.usda.gov

Appendix N: References for NPDES Permit Writers

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USDA NRCS Animal Feeding Operations (AFO) and Confined Animal Feeding Operations
(CAFO)
CNMP information
http://www.nrcs.usda.gov/technical/afo/
USDA NRCS Conservation Programs
http://www.nrcs.usda.gov/wps/portal/nrcs/main/?ss=16&navtype=BROWSEBYSUBJECT&cid=null
&navid=100120000000000&pnavid=100000000000000&position=BROWSEBYSUBJECT&ttype=
main&pname=Financial Assistance | NRCS
Environmental Quality Incentives Program
http://www.nrcs.usda.gov/programs/eqip/
Agricultural Management Assistance Program
http://www.nrcs.usda.gov/wps/portal/nrcs/main/?ss=16&navid=100120240000000&pnavid=
100120000000000&position=SUBNAVIGATION&ttype=main&navtype=SUBNAVIGATION&
pname=Agricultural Management Assistance
Wildlife Habitat Incentives Program
http://www.nrcs.usda.gov/wps/portal/nrcs/main/?ss=16&navid=100120340000000&pnavid=
100120000000000&position=SUBNAVIGATION&ttype=main&navtype=SUBNAVIGATION&
pname=Wildlife Habitat Incentives Program
USDA NRCS Animal Feeding Operations (AFO) and Confined Animal Feeding Operations
(CAFO)
CNMP information
http://www.nrcs.usda.gov/technical/afo/
USDA NRCS CNMP Technical Guidance
USDA’s General Manual, Title 190 – Part 405 Comprehensive Nutrient Management Plan
Technical Criteria
http://directives.sc.egov.usda.gov/26583.wba
USDA NRCS Nutrient Management Technical Practice Standard 590
USDA NRCS Nutrient Management Technical Resources, Conservation Practice Standard,
Code 590.
ftp://ftp-fc.sc.egov.usda.gov/NHQ/practice-standards/standards/590.pdf
USDA NRCS Nutrient Management Technical Resources
This website provides computer-based tools to facilitate the development and implementation of
NMPs.
http://www.nrcs.usda.gov/technical/nutrient.html

Appendix N: References for NPDES Permit Writers

N-4

NPDES Permit Writers’ Manual for CAFOs

NRCS National Engineering Handbook Part 651
Agricultural Waste Management Field Handbook
http://www.wsi.nrcs.usda.gov/products/w2q/awm/handbk.html
USDA Agricultural Research Service
http://www.ars.usda.gov
USDA NIFA, formerly Cooperative State Research, Education, and Extension Service
http://www.csrees.usda.gov/
USDA NIFA Cooperative Extension System Offices
The Cooperative Extension System is a nationwide non-credit educational network.
http://nifa.usda.gov/Extension/index.html
USDA Farm Service Agency
http://fsa.usda.gov/
USDA Farm Service Agency, Conservation Reserve Program
http://www.fsa.usda.gov/FSA/webapp?area=home&subject=copr&topic=crp
USDA Farm Service Agency, Conservation Reserve Enhancement Program
http://www.fsa.usda.gov/FSA/webapp?area=home&subject=copr&topic=cep
USDA National Nutrient Management Policy
USDA’s General Manual, Title 190 – Part 402 Nutrient Management
http://www.nrcs.usda.gov/technical/ecs/nutrient/gm-190.html
USDA Technical Service Providers (TSP) Registry
http://techreg.usda.gov/
State NRCS Field Office Technical Guidance
Click on the map to find available technical guidance for states and counties.
http://www.nrcs.usda.gov/technical/efotg/

Associations and Trade Groups
American Egg Board
http://aeb.org/
American Society of Agronomy (ASA)
http://www.agronomy.org/

Appendix N: References for NPDES Permit Writers

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Association of State and Interstate Water Pollution Control Agencies (ASIWPCA)
http://www.asiwpca.org/
Certified Crop Advisors (CCA)
https://www.agronomy.org/certifications
Certified Professional Agronomists (CPAg)
https://www.agronomy.org/certifications
Certified Professional Crop Scientists (CPCSc)
https://www.agronomy.org/certifications
Certified Professional Soil Scientists (CPSSc)
https://www.agronomy.org/certifications
ISO 14001
This website provides information on ISO 14001 and other standards from the International
Standards Organization.
http://www.iso.org/iso/home.htm
National Alliance of Independent Crop Consultants (NAICC)
http://www.naicc.org/
National Association of Conservation Districts (NACD)
http://www.nacdnet.org
National Association of State Departments of Agriculture (NASDA)
http://www.nasda.org
National Cattleman’s Beef Association (NCBA)
http://www.beef.org
National Milk Producers Federation (NMPF)
http://www.nmpf.org
National Pork Producers Council (NPPC)
http://www.nppc.org
National Turkey Federation (NTF)
http://www.turkeyfed.org
United States Poultry and Egg Association
http://www.poultryegg.org

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Other References
Land Grant Universities
This National Institute of Food and Agriculture (NIFA) website provides directory of land-grant
universities. To see a list of land-grant university websites, click a state.
http://www.csrees.usda.gov/qlinks/partners/state_partners.html
2010 Manure Analysis Proficiency Laboratories
http://www2.mda.state.mn.us/webapp/lis/manurelabs.jsp
The North American Proficiency Testing (NAPT) Program
http://www.naptprogram.org/
USDA and EPA Livestock and Poultry Environmental Stewardship Curriculum
This resource also includes the Livestock and Poultry Environmental Stewardship Program—
Lesson 51- Mortality Management
(http://www.extension.org/mediawiki/files/a/a8/LES_51.pdf)
http://www.lpes.org/
USDA Agricultural Research Service and Washington State University
Soil Plant Air Water (SPAW) Hydrology Model
http://hydrolab.arsusda.gov/SPAW/Index.htm

Appendix N: References for NPDES Permit Writers

NPDES Permit Writers’ Manual for CAFOs

Appendix
Sample Site-Specific
NPDES General Permit

O

NPDES Permit Writers’ Manual for CAFOs

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NPDES Permit Writers’ Manual for CAFOs

SAMPLE
NPDES GENERAL PERMIT
FOR
CONCENTRATED ANIMAL FEEDING OPERATIONS (CAFOs)
[US ENVIRONMENTAL PROTECTION AGENCY]
AUTHORIZATION TO DISCHARGE UNDER THE
NATIONAL POLLUTANT DISCHARGE ELIMINATION SYSTEM (NPDES)
[The intent of this sample NPDES General Permit for CAFOs is to recommend specific permit
requirements that are consistent with the NPDES CAFO regulations, CAFO ELG, the NPDES CAFO
Permit Writers’ Guidance including the sample Nutrient Management Plan and Technical Standard.
U.S. Environmental Protection Agency encourages permitting authorities to use the recommendations
of the guidance manual and this example permit as appropriate. Minimum NPDES permitting
requirements for CAFOs are defined at 40 CFR Parts 122, 123, and 412 and all other applicable CWA
regulations.]
In compliance with provisions of the Clean Water Act, 33 United States Code (U.S.C.) 1251 et seq. (the
Act), owners and operators of concentrated animal feeding operations (CAFOs) in [State], except those
CAFOs excluded from coverage in Part I of this permit, are authorized to discharge and must operate their
facility in accordance with effluent limitations, monitoring requirements, and other provisions set forth
herein.
A copy of this permit must be kept by the permittee at the site of the permitted activity.
This permit will become effective July 1, 2009.
This permit and the authorization to discharge under the NPDES permit shall expire at midnight June 30,
2014
Signed this [DAY] of [MONTH] and [YEAR]
[PERMITTING AUTHORITY—OFFICIAL]

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Contents
Part I.

Permit Area and Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-3
A. Permit Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-3
B. Permit Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-3
C. Eligibility for Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-3
D. Limitations on Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-3
E. Application for Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-5
F. Requiring an Individual Permit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-6
G. Permit Expiration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-7
H. Change in Ownership . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-7
I. Termination of Permit Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-7

Part II.

Effluent Limitations and Standards and Other Legal Requirements . . . . . . . . . . . . . . . O-8
A. Effluent Limitations and Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-8
B. Other Legal Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-14

Part III. Effluent Limitations and Standards of the Nutrient Management Plan . . . . . . . . . . . . . O-14
A. Procedural Requirements for Implementing the Terms of the Nutrient
Management Plan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-14
B. Site-Specific Terms of the Nutrient Management Plan . . . . . . . . . . . . . . . . . . . . . . . O-21
Part IV. Special Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-24
A. Facility Closure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-24
B. Additional Special Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-25
Part V.

Discharge Monitoring and Notification Requirements . . . . . . . . . . . . . . . . . . . . . . . O-27
A. Notification of Discharges Resulting from Manure, Litter, and Process
Wastewater Storage, Handling, On-site Transport and Application . . . . . . . . . . . . . . O-27
B. Monitoring Requirements for All Discharges from Retention Structures . . . . . . . . . . . O-27
C. General Inspection, Monitoring, and Record-Keeping Requirements . . . . . . . . . . . . O-28

Part VI. Annual Reporting Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-31
Part VII. Standard Permit Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-32
A. General Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-32
B. Proper Operation and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-35
C. Monitoring and Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-35
D. Reporting Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-36
E. Signatory requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-38
F. Availability of Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-39
G. Penalties for Violations of Permit Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-39
Part VIII. Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-40
Appendix A. Form 2B/Notice of Intent or Appropriate State Form . . . . . . . . . . . . . . . . . . . . . O-43
Appendix B. Technical Standards for Nutrient Management . . . . . . . . . . . . . . . . . . . . . . . . . O-44
Appendix C. Historic Properties Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-119
Appendix D. Notice of Termination Form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . O-120

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Part I. Permit Area and Coverage
A. Permit Area
This permit offers statewide NPDES permit coverage for discharges from operations defined as
concentrated animal feeding operations (CAFOs) in [State X].

B. Permit Coverage
This permit covers any operation that meets the following criteria:
1. Is located in the permit area as defined by Part I.A. of this permit,
2. That meets the definition of a CAFO at 40 CFR part 122.23(b)(4) large concentrated
animal feeding operation (see Part VIII, Definitions, large CAFO of this permit).
3. Discharges pollutants to waters of the United States. Once an operation is defined
as a CAFO, the NPDES requirements for CAFOs apply with respect to all animals in
confinement at the operation and all manure, litter and process wastewater generated
by those animals or the production of those animals, regardless of the type of animal.
4. Is eligible for permit coverage as defined in Part I.C of this permit.
5. Is authorized for permit coverage by the permitting authority as specified in Part I.F of
this permit.

C. Eligibility for Coverage
Unless excluded from coverage in accordance with Paragraph D or F below, owners/operators of
existing, currently operating animal feeding operations that are defined as CAFOs or designated
as CAFOs by the Permitting Authority (See Part VIII Definitions, CAFOs of this permit) and that
are subject to 40 CFR part 412, subpart C (Dairy Cows and Cattle Other than Veal Calves) are
eligible for coverage under this permit. Eligible CAFOs may apply for authorization under the
terms and conditions of this permit, by submitting a Notice of Intent (NOI) to be covered by this
permit (see Appendix A of this permit).
CAFO owners/operators may also seek to be excluded from coverage under this permit by (1) submitting to the permitting authority a Notice of Termination form (see Appendix D of this permit)
or (2) by applying for an individual NPDES Permit in accordance with Part I.F of this permit.

D. Limitations on Coverage
The following CAFOs are not eligible for coverage under this NPDES general permit and must
apply for an individual permit:
1. CAFOs that have been notified by the permitting authority to apply for an individual
NPDES permit in accordance with Part I.F (below) of this permit.

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Part I. Permit Area and Coverage

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2. CAFOs that have been notified by the permitting authority that they are ineligible for
coverage because of a past history of non-compliance.
3. Horse, Sheep, Duck, Veal, Poultry or Swine CAFOs.
4. Discharges that will adversely affect any species that are federally-listed as endangered
or threatened (“listed”) under the Endangered Species Act (ESA) and will result in the
adverse modification or destruction of habitat that is federally-designated as “critical
habitat” under the ESA. CAFOs seeking coverage under this general permit must follow
the conditions outlined in Part IV.B.5 of this permit.
5. CAFOs that do not meet the National Historic Preservation Act eligibility provisions
contained in Appendix C of this permit.
6. New dischargers to water quality impaired water (CWA, 303d list) unless the operator
performs one of the following:
a. Prevents any discharge that contains pollutant(s) for which the waterbody is
impaired, and includes documentation of procedures taken to prevent such
discharge in the NMP.
b. Documents that the pollutant(s) for which the waterbody is impaired is not present
at the facility, and retains documentation of this finding with the NMP.
c. In advance of submitting the NOI, provides to the permitting authority data to
support a showing that the discharge is not expected to cause or contribute to an
exceedance of a water quality standard, and retains such data onsite with the NMP.
To do this, the operator must provide data and other technical information to the
permitting authority sufficient to demonstrate one of the following:
i. For discharges to waters without an U.S. Environmental Protection Agency
approved or established TMDL, that the discharge of the pollutant for which
the water is impaired will meet in-stream water quality criteria at the point of
discharge to the waterbody.
ii. For discharges to waters with an U.S. Environmental Protection Agency
approved or established TMDL, that there are sufficient remaining
wasteload allocations in an U.S. Environmental Protection Agency approved
or established TMDL to allow the facility’s discharge and that existing
dischargers to the waterbody are subject to compliance schedules designed to
bring the waterbody into attainment with water quality standards.

Operators are eligible under this section if they receive an affirmative determination
from the permitting authority that the discharge will not contribute to the existing
impairment, in which case the operator must maintain such determination onsite with
the NMP.

7. CAFOs with discharges subject to New Source Performance Standards (NSPS) at
40 CFR part 412.

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E. Application for Coverage
1. Owners/operators of CAFOs seeking to be covered by this permit must:
a. For facilities covered by and/or expired permit that wish to have continuous permit
coverage, submit an NOI to the permitting authority by [DATE].
b. Submit a Nutrient Management Plan (NMP) with the NOI that meets the
requirements of 40 CFR parts 122 and 412, where applicable.
c. CAFO owners/operators may submit an NOI after the applicable date in Part I.E.1.a.
of this permit. Regardless of when the NOI is submitted, the CAFO’s authorization
under this permit is only for discharges that occur after permit coverage is granted.
The permitting authority reserves the right to take appropriate enforcement actions
for any unpermitted discharges.
d. If a CAFO has submitted an application for coverage under an individual permit
prior to issuance of the general permit and is seeking to be covered by this general
permit, the CAFO must submit an NOI for coverage.
2. Contents of the NOI: The NOI submitted for coverage under this permit must include
the following information:
a. Name of the owner or operator.
b. Facility location and mailing addresses.
c. Latitude and longitude of the production area (entrance to production area).
d. Topographic map of the geographic area in which the CAFO is located showing the
specific locations of the production area, land application area, and the name and
location of the nearest surface waters.
e. A diagram of the production area.
f. Number and type of animals, whether in open confinement or housed under roof
(beef cattle, broilers, layers, swine weighing 55 pounds or more, swine weighing
less than 55 pounds, mature dairy cows, dairy heifers, veal calves, sheep and
lambs, horses, ducks, turkeys, other).
g. Type of containment and storage (anaerobic lagoon, roofed storage shed, storage
ponds, under floor pits, aboveground storage tanks, belowground storage tanks,
concrete pad, impervious soil pad, other) and total capacity for manure, litter, and
process wastewater storage (tons/gallons).
h. Total number of acres under control of the applicant available for land application
of manure, litter, or process wastewater.
i. Estimated amounts of manure, litter, and process wastewater generated per year
(tons/gallons).

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j. Estimated amounts of manure, litter and process wastewater transferred to other
persons per year (tons/gallons).
k. An NMP that meets the requirements of the provisions of 40 CFR part 122.42(e)
(including, for all CAFOs subject to 40 CFR part 412, subpart C or subpart D, the
requirements of 40 CFR part 412.4(c), as applicable) and Part III of this permit.
3. Signature Requirements: The NOI must be signed by the owner/operator or other
authorized person in accordance with Part VII.E of this permit.
4. Where to Submit: Signed copies of the NOI or individual permit application must be
sent to: [PERMITTING AUTHORITY MAILING ADDRESS]
5. Upon receipt, the permitting authority will review the NOI and NMP to ensure that
the NOI and NMP are complete. The permitting authority may request additional
information from the CAFO owner or operator if additional information is necessary to
complete the NOI and NMP or to clarify, modify, or supplement previously submitted
material. If the permitting authority makes a preliminary determination that the
NOI is complete, the NOI, NMP and draft terms for the NMP to be incorporated into
the permit will be made available for a thirty (30) day public review and comment
period. The process for submitting public comments and requests of hearing will
follow the procedures applicable to draft permits as specified by 40 CFR parts 124.11
through 124.13. The permitting authority will respond to comments received during
the comment period as specified in 40 CFR part 124.17 and, if necessary, require the
CAFO owner or operator to revise the NMP in order to granted permit coverage. If
determined appropriate by the permitting authority, CAFOs will be granted coverage
under this general permit upon written notification by the permitting authority. The
permitting authority will identify the terms of the NMP to be incorporated into the
permit in the written notification.

F. Requiring an Individual Permit
1. The permitting authority may at any time require any facility authorized by this permit
to apply for, and obtain, an individual NPDES permit. The permitting authority will
notify the operator, in writing, that an application for an individual permit is required
and will set a time for submission of the application. Coverage of the facility under
this general NPDES permit is automatically terminated when (1) the operator fails to
submit the required individual NPDES permit application within the defined time
frame; or (2) the individual NPDES permit is issued by the permitting authority.
2. Any owner/operator covered under this permit may request to be excluded from the
coverage of this permit by applying for an individual permit. The owner/operator
shall submit an application for an individual permit (Form 1 and Form 2B) with the
reasons supporting the application to the permitting authority. If a final, individual
NPDES permit is issued to an owner/operator otherwise subject to this general permit,

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the applicability of this NPDES CAFO general permit to the facility is automatically
terminated on the effective date of the individual NPDES permit. Otherwise, the
applicability of this general permit to the facility remains in full force and effect (for
example, if an individual NPDES permit is denied to an owner/operator otherwise
subject to this general permit).

G. Permit Expiration
This permit will expire 5 years from the effective date. The permittee must reapply for permit
coverage 180 days before the expiration of this permit unless the permit has been terminated
consistent with § 122.64(b) or the CAFO will not discharge upon expiration of the permit. If this
permit is not reissued or replaced before the expiration date, it will be administratively continued
in accordance with the Administrative Procedures Act and remain in force and effect. Any
permittee who is granted permit coverage before the expiration date will automatically remain
covered by the continued permit until the earlier of any of the following:
1. Reissuance or replacement of this permit, at which time the permittee must comply
with the NOI conditions of the new permit to maintain authorization to discharge.
2. Issuance of an individual permit for the permittee’s discharges.
3. A formal decision by the permitting authority not to reissue this general permit, at
which time the permittee must seek coverage under an individual permit.
4. The permitting authority grants the permittee’s request for termination of permit
coverage.

H. Change in Ownership
If a change in the ownership of a facility whose discharge is authorized under this permit occurs,
coverage under the permit will automatically transfer if (1) the current permittee notifies the
permitting authority at least 30 days prior to the proposed transfer date; (2) the notice includes a
written agreement between the existing and new permittees containing a specific transfer date
for permit responsibility, coverage, and liability; and (3) the permitting authority does not notify
the existing permittee and the proposed new permittee of its intent to modify or revoke and
reissue the permit. If the new CAFO owner or operator modifies any part of the NMP, the NMP
shall be submitted to the permitting authority in accordance with Part III.A. of this permit and
40 CFR part 122.42(e)(6).

I. Termination of Permit Coverage
1. Coverage under this permit may be terminated in accordance with 40 CFR part 122.64
and if EPA determines in writing that one of the following three conditions are met:
a. The facility has ceased all operations and all wastewater or manure storage
structures have been properly closed in accordance with Natural Resource

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Conservation Service (NRCS) Conservation Practice Standard No. 360, Closure of
Waste Impoundments, as contained in the Natural Resources Conservation Service
Field Office Technical Guide and all other remaining stockpiles of manure, litter, or
process wastewater not contained in a wastewater or manure storage structure are
properly disposed.
b. The facility is no longer a CAFO that discharges manure, litter, or process
wastewater to waters of the United States.
c. In accordance with 40 CFR part 122.64, the entire discharge is permanently
terminated by elimination of the flow or by connection to a publicly owned
treatment works (POTW).

Part II. Effluent Limitations and Standards and Other
Legal Requirements
A. Effluent Limitations and Standards
The following effluent limitations apply to facilities covered under this permit:
1. Technology-based Effluent Limitations and Standards—Production Area
The CAFO must implement the terms of an NMP, as specified below and in Part III.B of
this permit.
a. There may be no discharge of manure, litter, or process wastewater pollutants into
waters of the United States from the production area except as provided below:

Whenever precipitation causes an overflow of manure, litter, or process
wastewater, pollutants in the overflow may be discharged into waters of the United
States provided:
i. The production area is properly designed, constructed, operated and
maintained to contain all manure, litter, process wastewater and the runoff
and direct precipitation from the 25-year, 24-hour storm event for the location
of the CAFO.
ii. The design storage volume is adequate to contain all manure, litter, and
process wastewater accumulated during the storage period including, at a
minimum, the following:
• The volume of manure, litter, process wastewater, and other wastes
accumulated during the storage period.
• Normal precipitation less evaporation during the storage period.
• Normal runoff during the storage period.
• The direct precipitation from the 25-year, 24-hour storm.
• The runoff from the 25-year, 24-hour storm event from the production area.

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• Residual solids after liquid has been removed.
• Necessary freeboard to maintain structural integrity.
• A minimum treatment volume, in the case of treatment lagoon.
b. Installation of a depth marker in all open surface liquid impoundments. The depth
marker must clearly indicate the minimum capacity necessary to contain the
runoff and direct precipitation of the 25-year, 24-hour rainfall event. The marker
shall be visible from the top of the levee.
c. Weekly visual inspections of all stormwater diversion devices, runoff diversion
structures, and devices channeling contaminated stormwater to the wastewater
and manure storage and containment structures are conducted.
d. Weekly inspections of the manure, litter, and process wastewater impoundments
noting the level as indicated by the depth marker installed in accordance with
Part II.A.1.b of this permit are conducted.
e. Daily visual inspections of all water lines, including drinking water and cooling
water lines are conducted.
f. Any deficiencies that are identified in daily and weekly inspections are corrected in
a timely manner.
g. Dead animals are properly disposed of within three (3) days unless otherwise
provided for by the permitting authority. Mortalities must not be disposed of in
any liquid manure or process wastewater system that is not specifically designed
to treat animal mortalities. Animals shall be disposed of in a manner to prevent
contamination of waters of the United States or creation of a public health hazard.
h. Complete, on-site records documenting implementation of all required additional
measures for a period of 5 years, including the records specified for Operation and
Maintenance in Part V.C, Table V-A of this permit are maintained.
i. The production area must be operated in accordance with the additional measures
and records specific in Part II.A.2 of this permit.
2. Additional Measures—Applicable to the Production Area
In addition to meeting the requirements in Part III.B below, the permittee must
implement the following additional measures:
a. Ensure adequate storage of manure, litter, and process wastewater, including
procedures to ensure proper operation and maintenance of the storage facilities.
b. Mortality handling practices shall be in accordance with all applicable state
and local regulatory requirements. Any such state/local requirements should be
consistent with NRCS Practice Standard 316 as applicable.
c. Ensure that clean water is diverted, as appropriate, from the production area in
accordance with Part III.A.3.c of this permit.

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d. Prevent direct contact of confined animals with waters of the United States.
e. Ensure that chemicals and other contaminants handled on-site are not
disposed of in any manure, litter, process wastewater, or storm water storage or
treatment system unless specifically designed to treat such chemicals and other
contaminants.
f. Identify specific records that will be maintained to document the implementation
and management of Part II.A.2. a through e of this permit.
g. In cases where CAFO-generated manure, litter, or process wastewater is sold or
given away the permittee must comply with the following conditions:
i. Maintain records showing the date and amount of manure, litter, and/or
process wastewater that leaves the permitted operation.
ii. Record the name and address of the recipient.
iii. Provide the recipient(s) with representative information on the nutrient
content of the manure, litter, and/or process wastewater.
iv. The records must be retained on-site, for a period of 5 years, and be submitted
to the permitting authority on request.
3. Water Quality-based Effluent Limitations and Standards—Production Area
The permitting authority has established the following permit conditions to protect
water quality standards.
a. Discharges to Water Quality Impaired Waters
i. If the CAFO discharges to an impaired water with an EPA approved or
established TMDL, EPA will inform the facility if any additional limits or
controls are necessary for the discharge to be consistent with the assumptions
of any available wasteload allocation in the TMDL, or if coverage under an
individual permit is necessary in accordance with Part I.F of this permit. Any
additional limits or controls shall be included in the NMP.
ii. If the CAFO discharges to an impaired water without an EPA approved or
established TMDL, EPA will inform the facility if any additional limits or
controls are necessary to meet water quality standards, or if coverage under an
individual permit is necessary in accordance with Part I.F of this permit. Any
additional limits or controls shall be included in the NMP.
iii. If a CAFO’s authorization for coverage under this permit relied on Part I.D.6
of this permit for a new discharge to an impaired water, the facility must
implement and maintain any control measures or conditions on its site that
enabled the CAFO to become eligible under Part I.D.6 of this permit, and shall
include these control measures or conditions in its NMP.
iv. If at any time the facility becomes aware, or EPA determines, that a discharge
to an impaired water has occurred and the requirements of Part II.A.3.a.i-iii of

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NPDES Permit Writers’ Manual for CAFOs

this permit have not been addressed, the facility must take corrective action to
fulfill the requirements of Part II.A.3.a.i-iii of this permit. Any changes to the
NMP required to fulfill the requirements of Part II.A.3.a.i-iii of this permit shall
be done in accordance with Part III.A.7 of this permit.
b. Tier 2 Antidegradation Requirements for New or Increased Dischargers
i. If the CAFO discharges directly to waters designated by a State or Tribe as Tier
2 or Tier 2.5 for antidegradation purposes under 40 CFR part 131.12(a) (see list
of Tier 2 and 2.5 waters on EPA’s website at http://www.U.S. Environmental
Protection Agency.gov/npdes/stormwater/msgp), the permitting authority may
notify the facility that additional analyses, control measures, or other permit
conditions are necessary to comply with the applicable antidegradation
requirements, or notify you that an individual permit application is necessary
in accordance with Part I.F of this permit. Any such additional requirements
shall be included in the NMP.
4. Technology-based Effluent Limitations and Standards—Land Application Areas
under the Control of the CAFO Owner/Operator
Permittees that apply manure, litter, or process wastewater to land under the
permitted CAFO’s ownership or operational control must implement the terms of an
NMP, as specified below and in Part III.B of this permit. The NMP must be developed
in accordance with the requirements of this section and Part III.A of this permit.
a. Determination of application rates. Application rates for manure, litter, or
process wastewater must minimize phosphorus and nitrogen transport from the
field to surface waters in compliance with the technical standards for nutrient
management established by the permitting authority, as follows:
i. Application rates must be determined in accordance with the result of the Iowa
Phosphorus Index as specified in IAC Chapter 567—65.17(17).
ii. Realistic yield goals must be established in accordance with the procedures in
IAC Chapter 567—65.17(6).
iii. The crop nutrient recommendations provided in Appendix A5, “Crop Nitrogen
Usage Rate Factors for Various Crops,” and Appendix A6, “Nutrient Removal
for Iowa Crops,” of Iowa DNR’s Manure Management Plan Form or Iowa State
University Extension publication PM-1688, “General Guide to Crop Nutrient
and Limestone Recommendations in Iowa,” must be used.
iv. Nitrogen credits for prior legume crops must be determined in accordance
with values specified in footnote t of Iowa DNR’s Manure Management Plan
form.
v. Nitrogen mineralization rates must be consistent with the ranges identified
in Iowa State University Extension publication PMR 1003, “Using Manure
Nutrients for Crop Production.”

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NPDES Permit Writers’ Manual for CAFOs

vi. Nitrogen loss factors must be consistent with those provided in Appendix A7,
“Nitrogen Application Losses,” of Iowa DNR’s Manure Management Plan Form.
vii. Timing and method of manure, litter, and process wastewater application must
be addressed in accordance with the criteria and considerations in Iowa NRCS
Conservation Practice Standard Code 590 (Nutrient Management).
viii.
For fields where P-based management is required, in accordance with
the out­come of the Iowa Phosphorus Index, multi-year phosphorus application
is per­mitted on fields that do not have a high potential for phosphorus runoff
to surface water. Such applications must be in accordance with the procedures
and limitations specified in footnote bb of Iowa DNR’s Manure Management
Plan Form.
b. Manure and soil sampling. Manure must be analyzed at least once annually
for nitrogen and phosphorus content in accordance with the manure testing
requirements of Iowa NRCS Conservation Practice Standard Code 590 (Nutrient
Management). Manure samples must be analyzed by a laboratory listed with
the Manure Testing Laboratory Certification Program (MTLCP). Soil must be
analyzed at least once every 4 years in accordance with soil testing requirements
established in IAC Chapter 567—65.17(16). The results of the analyses must be used
in determining application rates for manure, litter, and process wastewater.
c. Inspection of land application equipment for leaks. Equipment used for land
application of manure, litter, or process wastewater must be inspected periodically
for leaks.
d. Land application setback requirements. Manure, litter, or process wastewater
must not be applied closer than 100 feet to any downgradient water of the United
States, open tile line intake structures, sinkholes, agricultural well heads, or other
conduits to waters of the United States. The permittee may elect to use a 35-foot
vegetated buffer where applications of manure, litter, or process wastewater are
prohibited as an alternative to the 100-foot setback to meet the requirement. As a
compliance alternative, the permittee may demonstrate that a set-back or buffer
is not necessary because implementation of alternative conservation practices or
field-specific conditions will provide pollutant reductions equivalent or better than
the reductions that would be achieved by the 100-foot setback.
e. Record Keeping requirements. Complete, on-site records including the site-specific
NMP must be maintained to document implementation of all required land
application practices. Such documentation must include the records specified for
Soil and Manure/Wastewater Nutrient Analyses and Land Application in Part V.C,
Table V-A of this permit.

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5. Additional Measures—Applicable to the Land Application under the Control of the
CAFO Owner/Operator
a. Additional BMPs to control discharges from land application areas.
i. Areas shall be identified that, due to topography, activities or other factors,
have a high potential for significant soil erosion. Where these areas have the
potential to contribute pollutants to waters of the United States, measures used
to limit erosion and pollutant runoff shall be identified.
ii. Irrigation systems shall be managed so as to minimize (a) ponding or puddling
of wastewater on land application fields, (b) contamination of ground and
surface water and (c) the occurrence of nuisance conditions, such as odors and
flies.
b. Prohibitions
i. There shall be no discharge of manure, litter, or process wastewater to waters of
the United States from a CAFO as a result of the application of manure, litter or
process wastewater to land areas under the control of the CAFO, except where
it is an agricultural stormwater discharge. Where manure, litter, or process
wastewater has been applied in accordance with the terms of the NMP as set
forth in Part II.A. and III.B of this permit, a precipitation related discharge of
manure, litter, or process wastewater from land areas under the control of the
CAFO is considered to be an agricultural stormwater discharge.
ii. Nutrients and organic nutrient sources shall not be surface applied to frozen,
snow covered ground, or saturated soil if a potential risk for runoff exists.
A potential risk for runoff exists on slopes greater than 5% unless erosion is
controlled to soil loss tolerance levels (“T”) or less. Manure may be surface
applied to frozen, snow covered or saturated ground if a potential risk for
runoff exists only under one of the following conditions with the permission of
the permitting authority:
• Where manure storage capacity is insufficient and failure to surface apply
creates a risk of an uncontrolled release of manure.
• On an emergency basis.
6. Water Quality-based Effluent Limitations and Standards–Applicable to the Land
Application under the Control of the CAFO Owner/Operator
There shall be no unauthorized dry weather discharges from land application sites.
7. Effluent Limitations–Other Discharges
a. Process wastewater discharges from outside the production area, including
washdown of equipment that has been in contact with manure, raw materials,
products or byproducts that occurs outside of the production area and runoff of
pollutants from raw materials, products or byproducts (such as manure, feathers,
litter, bedding and feed) from the CAFO that have been spilled or otherwise

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deposited outside the production area and which are discharged to waters of the
United States, shall be identified in the NMP. The NMP shall identify measures
necessary to meet applicable water quality standards.
b. Discharges that do not meet the definition of process wastewater, including:
(1) discharges associated with feed, fuel, chemical, or oil spills, equipment repair,
and equipment cleaning, where the equipment has not been in contact with
manure, raw materials, products or byproducts; and (2) domestic wastewater
discharges to waters of the United States shall be identified in the NMP. The NMP
shall identify measures necessary to meet applicable water quality standards.
c. Storm water discharges that are not addressed under the effluent limitations in
Part II.A.1-6 of this permit, remain subject to applicable industrial or construction
storm water discharge requirements.
In addition to meeting the above effluent limitations in Part II.A of this permit, the permittee
must comply with the special conditions established in Part IV of this permit.

B. Other Legal Requirements
No condition of this permit shall release the permittee from any responsibility or requirements
under other statutes or regulations, federal, state/Indian tribe or local.

Part III. Effluent Limitations and Standards of the
Nutrient Management Plan
A. Procedural Requirements for Implementing the Terms of
the Nutrient Management Plan
CAFO owners or operators seeking coverage under this general permit must submit a Nutrient
Management Plan (NMP) with the NOI, as required by Part I.E.1. of this permit. The NMP shall
specifically identify and describe practices that will be implemented to assure compliance with
the effluent limitations and other conditions of this permit set forth in this part and Part II.A of
this permit (Effluent Limitations and Standards). The NMP must be developed in accordance with
the technical standards for nutrient management identified in Appendix B of this permit.
1. Schedule. The completed NMP must be submitted to the permitting authority with
the NOI for CAFOs seeking coverage under this permit. The CAFO shall implement its
NMP upon authorization under this permit, in accordance with the terms of the NMP
set forth in Part III.B of this permit.
2. NMP Review and Terms.
a. Upon receipt of the NMP, the permitting authority will review the NMP. The
permitting authority may request additional information from the CAFO owner or

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operator if additional information is necessary to complete the NMP, or to clarify,
modify, or supplement previously submitted material, the Director may request
such information from the CAFO owner or operator.
b. The permitting authority will use the NMP to identify site-specific permit terms to
be incorporated into this permit. The permitting authority will identify site-specific
permit terms with respect to protocols for the land application of manure, litter,
and process wastewater. The permitting authority will also identify site-specific
permit terms with respect to manure, litter, and process wastewater storage
capacities and site-specific conservation practices on the basis of the CAFO’s
NMP to the extent that such terms are necessary to support the application rates
expressed in the NMP. The permitting authority will also identify site-specific
permit terms with respect to mortality management, clean water diversions,
preventing direct contact of animals with waters of the United States, chemical
handling, protocols for manure and soil testing, and record keeping as appropriate.
c. When the permitting authority determines that the NMP and notice of intent
are complete, the permitting authority will make available to the public the NOI
submitted by the CAFO, including the CAFO’s NMP, and the terms of the NMP to
be incorporated into the permit, as determined by the permitting authority. The
permitting authority will notice the proposal to grant coverage under the permit
and the availability of the aforementioned documentation for public review and
comment. The notice will also provide the opportunity for a public hearing on the
NOI and draft NMP in accordance with 40 CFR parts 124.11 and 12.
d. The period for the public to comment and request a hearing on the proposed terms
of the NMP to be incorporated into the permit shall be thirty (30) days.
e. The permitting authority will respond to comments received during the comment
period, as provided in 40 CFR part 124.17, and, if necessary, require the CAFO
owner or operator to revise the NMP to be granted permit coverage.
f. When the permitting authority authorizes the CAFO owner or operator to
discharge under the general permit, the terms of the NMP shall be incorporated
as terms and conditions of the permit for the CAFO. The permitting authority will
notify the CAFO owner or operator that coverage has been authorized and of the
applicable terms and conditions of the permit. Those site-specific permit terms will
be provided to the permittee in a written permit authorization notice which will be
included as Part III.B of this permit.
g. Each CAFO covered by this permit must comply with the site-specific permit terms
established by the permitting authority on the basis of the CAFO’s site-specific NMP.
3. NMP Content. The site-specific NMP at a minimum must include practices and
procedures necessary to implement the applicable effluent limitations and standards

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in Part II.A of this permit. In addition, the NMP and each CAFO covered by this permit
must, as applicable, do the following:
a. Ensure adequate storage of manure, litter, and process wastewater, including
procedures to ensure proper operation and maintenance of the storage facilities.
All wastewater and manure containment structures shall at a minimum be
designed, constructed, operated, and maintained in accordance with the
standards of the Natural Resources Conservation Service, Field Office Technical
Guide. Storage capacity must be sufficient to meet the minimum requirements of
Part II.A.1 of this permit and also must be sufficient to allow the CAFO to comply
with the land application schedule specified in the NMP. To the extent that the
NMP depends on off-site transport or other means of handling to ensure adequate
storage capacity this must be described in the NMP.

If the CAFO needs to maintain storage capacity that exceeds the minimum capacity
requirements of Part II.A.1 of this permit to comply with the land application provisions of the NMP, the storage capacity shall become a term of this permit and the
permitting authority will develop site-specific terms based on the submitted NMP.

b. Ensure proper management of mortalities (i.e., dead animals) to ensure that they
are not disposed of in a liquid manure, storm water, or process wastewater storage
or treatment system that is not specifically designed to treat animal mortalities.
Mortalities shall be handled in such a way as to prevent the discharge of pollutants
to waters of the United States.
c. Ensure that clean water is diverted, as appropriate, from the production area.
Any clean water that is not diverted and comes into contact with raw materials,
products, or by-products including manure, litter, process wastewater, feed, milk,
eggs, or bedding is subject to the effluent limitations specified in Part II.A of this
permit. Where clean water is not diverted, the CAFO owner or operator must
document that it has been accounted for in meeting the requirement to ensure
adequate storage capacity as a condition of this permit. Clean water includes, but is
not limited to, rain falling on the roofs of facilities and runoff from adjacent land.
d. Prevent the direct contact of animals confined or stabled at the facility with waters
of the United States.
e. Ensure that chemicals and other contaminants handled on-site are not disposed
of in any manure, litter, process wastewater, or stormwater storage or treatment
system unless specifically designed to treat such chemicals or contaminants. All
wastes from dipping vats, pest and parasite control units, and other facilities used
for the management of potentially hazardous or toxic chemicals shall be handled
and disposed of in a manner sufficient to prevent pollutants from entering the
manure, litter, or process wastewater retention structures or waters of the United
States. Include references to any applicable chemical handling protocols and
indicate that other protocols included in the NMP will be reviewed.

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f. Identify appropriate site-specific conservation practices to be implemented, including as appropriate buffers or equivalent practices, to control runoff of pollutants to
waters of the United States and specifically, to minimize the runoff of nitrogen and
phosphorus. Each CAFO covered by this permit must implement the site-specific
conservation practices determined by the permitting authority to be a term of this
permit, as specified in the CAFO’s permit authorization notice. Those practices may
include residue management, conservation crop rotation, grassed waterways, strip
cropping, vegetated buffers, riparian buffers, setbacks, terracing, and diversions.
g. Identify protocols for appropriate testing of manure, litter, process wastewater, and
soil. Manure, wastewater and soil sampling must be conducted in accordance with
the requirements of Part II.A.4.b. of this permit and the following protocols:
i. Manure, litter, and process wastewater must be sampled annually in
accordance with protocols established in Iowa NRCS Conservation Practice
Standard Code 590 (Nutrient Management) and Iowa State University
Extension publication  1558, “How to Sample Manure for Nutrient Analysis.”
ii. Manure, litter, and process wastewater must be analyzed, at a minimum, for
constituents identified in Iowa NRCS Conservation Practice Standard Code
590 (Nutrient Management) (total nitrogen, phosphorus, and potassium, and
percent moisture and/or percent solids) by a laboratory listed with the Manure
Testing Laboratory Certification Program (MTLCP).
iii. Soil must be sampled and analyzed at least once every four years in accordance
with protocols established in IAC Chapter 567—65.17(16).
h. Establish protocols to land apply manure, litter, or process wastewater in accordance with site-specific nutrient management practices that ensure appropriate
agricultural utilization of the nutrients in the manure, litter, or process wastewater.

The CAFO’s site-specific NMP shall document the calculation of land application
rates of manure, litter, or process wastewater. The technical standards identified
in Appendix B of this permit shall be used for calculating these rates. The rate
calculation shall address the form, source, amount, timing, and method of
application on each field to achieve realistic production goals while minimizing
nitrogen and phosphorus movement to surface water. The rate calculation shall be
based on the results of a field specific assessment of the potential for nitrogen and
phosphorus transport from the field to surface waters using the Iowa Phosphorus
Index, as specified in IAC Chapter 567—65.17(17).

Development of site-specific terms will be based on the permitting authority’s
review of the NMP submitted in accordance with the requirements of Parts I.E
and III.A of this permit. To support the development of site-specific terms the
submitted NMP must include at a minimum:
• Names of fields available for land application.

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• Field-specific rates of application properly developed as specified below, under
Narrative Rate Approach, in the following chemical forms in this part and
[nitrogen and phosphorus].
• The information specified for the narrative rate approach in the paragraph
below.
• Any additional information necessary to assess the adequacy of the application
rates included in the NMP.

Application rates should be expressed in NMPs consistent with the narrative rate
approach described below:

Narrative Rate Approach. Expresses a narrative rate of application that results in
the amount, in tons or gallons, of manure, litter, and process wastewater to be land
applied. The narrative rate approach must include in the NMP submitted to the
permitting authority the following information for each crop and field covered by
the NMP, which will be used by the permitting authority to establish site-specific
permit terms:
• The maximum amounts of nitrogen and phosphorus that will be derived from
all sources of nutrients (pounds/acre for each crop and field).
• The outcome of the field-specific assessment of the potential for nitrogen
and phosphorus transport from each field. The potential for nitrogen and
phosphorus transport shall be determined using the Iowa Phosphorus Index
as specified in IAC Chapter 567—65.17(17). The CAFO must specify any
conservation practices used in calculating the risk rating.
• The crops to be planted in each field or any other uses of a field such as pasture
or fallow fields, including alternative crops if applicable. Any alternative crops
included in the NMP must be listed by field, in addition to the crops identified
in the planned crop rotation for that field.
• The realistic annual yield goal for each crop or use identified for each field for
each year, including any alternative crops identified.
• The nitrogen and phosphorus recommendations from Appendix A5, “Crop
Nitrogen Usage Rate Factors for Various Crops,” and Appendix A6, “Nutrient
Removal for Iowa Crops,” to Iowa DNR’s Manure Management Plan Form
for each crop or use identified for each field, including any alternative crops
identified.
• The methodology (including formulas, sources of data, protocols for making
determination, etc.) and actual data that will be used to account for: (1) the
results of soil tests required by Parts II.A.4.b and III.A.3.g of this permit,
(2) credits for all nitrogen in the field that will be plant-available, (3) the amount
of nitrogen and phosphorus in the manure, litter, and process wastewater

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to be applied, (4) consideration of multi-year phosphorus application (for
any field where nutrients are applied at a rate based on the crop phosphorus
requirement, the methodology must account for single-year nutrient
applications that supply more than the crop’s annual phosphorus requirement),
(5) other additions of plant available nitrogen and phosphorus to the field
(i.e., from sources other than manure, litter, or process wastewater or credits
for residual nitrogen), (6) timing and method of land application, and (7)
volatilization of nitrogen and mineralization of organic nitrogen.
• Any other factors necessary to determine the amounts of nitrogen and
phosphorus to be applied in accordance with the Narrative Rate Approach

The NMPs must also include the following projections, which will not be used by
the permitting authority in establishing site-specific permit terms:
• Planned crop rotations for each field for the period of permit coverage.
• Projected amount of manure, litter, or process wastewater to be applied.
• Projected credits for all nitrogen in the field that will be plant-available.
• Consideration of multi-year phosphorus application.
• Accounting for other additions of plant-available nitrogen and phosphorus to
the field.
• The predicted form, source, and method of application of manure, litter, and
process wastewater for each crop.

4. Signature. The NMP shall be signed by the owner/operator or other signatory authority
in accordance with Part VII.E of this permit (Signatory Requirements).
5. A current copy of the NMP shall be kept on site at the permitted facility in accordance
with Part VIII.C of this permit and provided to the permitting authority upon request.
6. Recordkeeping Requirement.
a. All CAFOs using the narrative rate approach must calculate maximum amounts
of manure, litter, and process wastewater to be land applied at least once each
year using the methodology specified in the NMP pursuant to Part III.A.3.h of
this permit before land applying manure, litter, and process wastewater. Such
calculations must rely on the following data:
i. A field-specific determination of soil levels of nitrogen and phosphorus. For
nitrogen, the determination must include a concurrent determination of
nitrogen that will be plant available. For phosphorus, the determination must
include the results of the most recent soil test conducted as required in Parts
II.A.4.b and III.A.3.g of this permit,

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ii. The results of the most recent representative manure, litter, and process
wastewater tests for nitrogen and phosphorus taken within 12 months of
the date of land application, as required in Parts II.A.4.b and III.A.3.g of this
permit, in order to determine the amount of nitrogen and phosphorus in the
manure, litter, and process wastewater to be applied.
b. Identify and maintain all records necessary to document the development and
implementation of the NMP and compliance with the permit.
7. Changes to the NMP
a. When a CAFO owner or operator covered by this permit makes changes to the
CAFO’s NMP previously submitted to the permitting authority, the CAFO owner
or operator must provide the permitting authority with the most current version
of the CAFO’s NMP and identify changes from the previous version, except that
annual calculations of application rates for manure, litter, and process wastewater
as required in Part III.A.6.a of this permit are not required to be submitted to the
permitting authority.
b. When changes to an NMP are submitted to the permitting authority, the
permitting authority will review the revised NMP to ensure that it meets the
requirements of Parts II.A and III.A.3. If the permitting authority determines that
the changes to the NMP necessitate revision to the terms of the NMP incorporated
into the permit issued to the CAFO, the permitting authority must determine
whether such changes are substantial. Substantial changes to the terms of an NMP
incorporated as terms and conditions of a permit include, but are not limited to the
following:
i. Addition of new land application areas not previously included in the CAFO’s
NMP, except if the added land application area is covered by the terms of an
NMP incorporated into an existing NPDES permit and the CAFO complies
with such terms when applying manure, litter, and process wastewater to the
added land.
ii. For NMPs using the Narrative Rate Approach, changes to the maximum
amounts of nitrogen and phosphorus derived from all sources for each crop.
iii. Addition of any crop or other uses not included in the terms of the CAFO’s
NMP.
iv. Changes to site-specific components of the CAFO’s NMP, where such changes
are likely to increase the risk of nitrogen and phosphorus transport to waters of
the United States.
c. If the permitting authority determines that the changes to the terms of the NMP
are not substantial, the permitting authority will include the revised NMP in the
permit record, revise the terms of the permit on the basis of the site-specific NMP,

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and notify the CAFO and the public of any changes to the terms of the permit on
the basis of revisions to the NMP.
d. If the permitting authority determines that the changes to the terms of the
NMP are substantial, the permitting authority will notify the public, make the
proposed changes and the information submitted by the CAFO owner or operator
available for public review and comment, and respond to all significant comments
received during the comment period. The public notice will be provided using the
guidelines described in Part III.A.2.c of this permit. The permitting authority may
require the permittee to further revise the NMP, if necessary. Once the permitting
authority incorporates the revised terms of the NMP into the permit, the
permitting authority will notify the permittee of the revised terms and conditions
of the permit.

B. Site-Specific Terms of the Nutrient Management Plan
This permit specifically authorizes DEF Feedlot to discharge as of September 1, 2009 when the
facility is operating in compliance with the terms and conditions of this permit. The site-specific
terms of the NMP set forth in this section are applicable to DEF Feedlot:
1. The permittee must ensure adequate storage of manure, litter, and process wastewater,
including procedures to ensure proper operation and maintenance of the storage
facilities by complying with section 2.3 of the nutrient management plan.
2. The permittee must ensure proper management of mortalities by following NRCS IA
Standard 316, Animal Mortality Facility, October 2007 for proper management of dead
animals. Dead animals will be disposed of utilizing Valley Rendering Services. When
rendering services are used, dead animals will be picked up within 24 hours. Dead
animals will be stored in a separate bermed area adjacent to the production area to
control runoff. Adequate space must be available in the bermed area to hold normal
animal mortality at the feedlot operation. Process wastewater that runs off this area
must be collected and transported to the waste storage ponds. There are no additional
operation and maintenance activities required with plan to be used to address normal
animal mortality at the operation. Under no circumstances, will the manure treatment
systems be used to manage any mortality.
3. The permittee must ensure that clean water is diverted, as described in section 2.2 of
the nutrient management plan.
4. The permittee must ensure that chemicals and other contaminants handled on-site as
described in section 3.4 of the nutrient management plan.
5. The permittee must implement the following conservation practices:
6. The permittee will maintain the specific records required by section 7 of the NMP.

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7. The permittee will implement the following protocols to land apply manure, litter or
process wastewater to ensure appropriate agricultural utilization of the nutrients in
the manure, litter or process wastewater:
The methodology is expressed within Manure Management Planner (MMP) version 0.29. The
permitting authority has determined that the methodology used by MMP encompasses all the
factors of the methodology and the plan was developed in accordance with the State’s technical
standard. Additional site specific permit terms for expressing protocols for land application under
the narrative rate approach include:
Field

Area

Conservation Practice

NRCS Iowa Conservation Practice Reference

Bob’s Farm North –
8N

56.4
Acres

50ꞌ Stream Vegetated
Buffer

Riparian Forest Buffer (Ac.) (391)
(August 2007)

Contour Farming

Contour Farming (Ac.) (330) (May 2005)

Residue Management

Residue Management, Seasonal
(Ac.) (344) (March 2007)

50ꞌ Stream Vegetated
Buffer

Riparian Forest Buffer (Ac.) (391)
(August 2007)

Contour Farming

Contour Farming (Ac.) (330) (May 2005)

Residue Management

Residue Management, Seasonal
(Ac.) (344) (March 2007)

Bob’s Farm South –
8S

79.6
Acres

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Bob's
Farm
South

Field

8S

2014

2013

2012

2011

2010
79.6

P Loss
risk

Manure
Application
Rate

Outcome of the
assessment of the
potential for nutrient
transport

2. On an
emergency
basis

1. Where
manure storage
capacity is
insufficient
and failure to
surface apply
creates a risk of
an uncontrolled
release of
manure

Field slope 7%. Medium
Manure
shall not be
Manure may
applied in
only be surface
excess of
applied to this
field when
two times
the crop
the ground is
phosphorus
frozen, snow
covered or
removed with
crop harvest
saturated if one
of the following
over the
conditions
period of the
crop rotation
exists:

Timing limitations
Crop Total
for land
application
Subfield Year Acres

Fields available
for land
application

Soy­
bean

Corn

Soy­
bean

Corn

Soy­
bean

61 bu/
acre

195 bu/
acre

61 bu/
acre

195 bu/
acre

61 bu/
acre

Max lbs
N/acre
derived
from all
sources

Max lbs
P2O5/acre
derived
from all
sources
Crops

Yield
Goal

73 lbs P205
/acre

210 lbs N
/acre

Corn
Recommend­
ations:

49 lbs P205
/acre

Corn

41 ton/
acre

Soybean
Soybeans Soybeans Wheat 78 bu/
Recommend­
= 0 lbs
acre
= 0 lbs
ations:
Corn =
Corn =
232 lbs N
210 lbs
190 lbs
/acre

Total N and P
Planned Realistic recommend­
crops Annual ations for each
or other Yield
crop on each
use
Goal
field

205

88

51

41

lbs/acre

N Rec P Rec

Alternative Crops

NPDES Permit Writers’ Manual for CAFOs

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Appendix O: Sample Site-Specific NPDES General Permit
Part III. Effluent Limitations and Standards of the Nutrient Management Plan

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NPDES Permit Writers’ Manual for CAFOs

Part IV. Special Conditions
A. Facility Closure
The following conditions shall apply to the closure of lagoons and other earthen or synthetic lined
basins and other manure, litter, or process wastewater storage and handling structures:
1. Closure of Lagoons and Other Surface Impoundments
a. No lagoon or other earthen or synthetic lined basin shall be permanently
abandoned.
b. Lagoons and other earthen or synthetic lined basins shall be maintained at all
times until closed in compliance with this section.
c. All lagoons and other earthen or synthetic lined basins must be properly closed
if the permittee ceases operation. In addition, any lagoon or other earthen or
synthetic lined basin that is not in use for a period of 12 consecutive months must
be properly closed unless the facility is financially viable, intends to resume use
of the structure at a later date, and either (1) maintains the structure as though it
were actively in use, to prevent compromise of structural integrity; or (2) removes
manure and wastewater to a depth of one foot or less and refills the structure with
clean water to preserve the integrity of the synthetic or earthen liner. In either
case, the permittee shall notify the permitting authority within thirty (30) days of
basin closure detailing the actions taken, and shall conduct routine inspections,
maintenance, and record keeping as though the structure were in use. Prior
to restoration of use of the structure, the permittee shall notify the permitting
authority in writing and provide the opportunity for inspection.
d. All closure of lagoons and other earthen or synthetic lined basins must be
consistent with NRCS Conservation Practice Standard Code 360 (Closure of
Waste Impoundments). Consistent with this standard the permittee shall remove
all waste materials to the maximum extent practicable and dispose of them in
accordance with the permittee’s nutrient management plan, unless otherwise
authorized by the permitting authority.
e. Unless otherwise authorized by the permitting authority completion of closure
for lagoons and other earthen or synthetic lined basins shall occur as promptly
as practicable after the permittee ceases to operate or, if the permittee has not
ceased operations, 12 months from the date on which the use of the structure
ceased, unless the lagoons or basins are being maintained for possible future use
in accordance with the requirements above.
2. Closure Procedures for Other Manure, Litter, or Process Wastewater Storage and
Handling Structure

No other manure, litter, or process wastewater storage and handling structure shall
be abandoned. Closure of all such structures shall occur as promptly as practicable

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Part IV. Special Conditions

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NPDES Permit Writers’ Manual for CAFOs

after the permittee has ceased to operate, or, if the permittee has not ceased to operate,
within 12 months after the date on which the use of the structure ceased. To close a
manure, litter, or process wastewater storage and handling structure, the permittee
shall remove all manure, litter, or process wastewater and dispose of it in accordance
with the permittee’s NMP, or document its transfer from the permitted facility in
accordance with Manure Transfer requirements specified in Table V-A in Part V.C of
this permit unless otherwise authorized by the permitting authority.

B. Additional Special Conditions
1. Liner Requirement: The permittee shall document that no direct hydrologic
connection exists between the contained wastewater and surface waters of the United
States. Where the permittee cannot document that no direct hydrologic connection
through ground water exists, the ponds, lagoons and basins of the containment
facilities must have a liner which will prevent the potential contamination of surface
waters.
a. Documentation of no direct hydrologic connection. The permittee can document
lack of hydrologic connection by either: (1) documenting that there will be no
significant leakage from the retention structure; or (2) documenting that any
leakage from the retention structure would not migrate to surface waters. For
documentation of no significant leakage, in-situ materials must, at a minimum,
meet the minimum criteria for hydraulic conductivity and thickness described
in Part IV.B.1.b of this permit. Documentation that leakage will not migrate to a
surface water must include maps showing ground water flow paths, or that the
leakage enters a confined environment. This documentation must be certified
in writing by a NRCS engineer or a Professional Engineer and must include
information on the hydraulic conductivity and thickness of the natural materials
underlying and forming the walls of the containment structure up to the wetted
perimeter.
b. Liner Construction. Liners constructed and maintained in accordance with
NRCS design specifications shall be considered to prevent hydrologic connection
which could result in the contamination of surface waters. Where no site-specific
assessment has been done by a NRCS engineer or Professional Engineer, the liner
shall be constructed to have hydraulic conductivities no greater than 1x10 (-7) cm/
sec, with a thickness of 1.5 feet or greater or its equivalency in other materials.
c. Liner Maintenance. The permittee must maintain the liner to inhibit infiltration of
wastewaters. Liners shall be protected from animals by fences or other protective
devices. No tree shall be allowed to grow such that the root zone would intrude or
compromise the structure of the liner. Any mechanical or structural damage to the
liner must be evaluated by a NRCS Engineer or Professional Engineer within thirty
(30) days of the damage. Documentation of liner maintenance shall be kept with
the Nutrient Management Plan (NMP). The permittee shall have a NRCS Engineer

Appendix O: Sample Site-Specific NPDES General Permit
Part IV. Special Conditions

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NPDES Permit Writers’ Manual for CAFOs

or Professional Engineer review the documentation and do a site evaluation a mini­
mum of once every five (5) years. If notified by the permitting authority that a direct
hydrological connection to waters of the United States exists for the contamination
of surface waters or drinking water, the permittee shall install a leak detection
system or monitoring wells, or take other appropriate measures in accordance
with that notice. Documentation of compliance with the notification must be kept
with the NMP, as well as all sampling data. Data from the monitoring wells must
be kept on site for three (3) years with the NMP. The first year’s sampling shall be
considered the baseline data and must be retained on site for the life of the facility.
2. Retention Structure Dewatering. A schedule must be developed for liquid waste
removal from the retention structure(s). A date log indicating weekly inspection
of wastewater level in the retention facility, including specific measurement of
wastewater level must be kept. Retention facilities shall be equipped with either
irrigation or evaporation or liquid removal systems capable of dewatering the retention
facilities. Operators using pits, ponds, or lagoons for storage and treatment of storm
water, manure and process generated wastewater, including flush water waste
handling systems, shall maintain sufficient available storage capacity to contain
the runoff and the direct precipitation from a 25-year, 24-hour rainfall event. The
operator shall restore the storage capacity as soon as possible after any rainfall event or
accumulation of wastes reduces such storage capacity, weather permitting.
3. Spills. Appropriate measures necessary to prevent spills and to cleanup spills of
any toxic and other pollutants shall be taken. Handling procedures and storage for
these materials must be specified in the NMP. Procedures for cleaning up spills shall
be identified, and the necessary equipment to implement clean up shall be made
available to facility personnel. All spills and clean-up activities must be documented.
Documentation of spills and clean-up must be kept with the NMP.
4. Solids, sludges, manure or other pollutants removed in the course of treatment or
control of wastewaters shall be disposed of in a manner to prevent pollutants from
being discharged to waters of the United States.
5. Manure, litter, and process wastewater handling, treatment, and management
shall not result in the destruction or adverse modification of the critical habitat
of endangered or threatened species, or contribute to the taking of endangered or
threatened species of plant, fish or wildlife. The operator shall notify State and Federal
wildlife agencies, the permitting authority, and the U.S. Environmental Protection
Agency within 48 hours if any dead or injured threatened or endangered species or
protected migratory birds are observed in or on receiving waters following a discharge
or on the facility’s land application areas at any time.
6. Manure, litter, and process wastewater handling, treatment, and management
shall not create an environmental or public health hazard; shall not result in the
contamination of drinking water; shall conform to State guidelines and/or regulations
for the protection of surface water quality.

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Part IV. Special Conditions

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NPDES Permit Writers’ Manual for CAFOs

7. Employee Training. Employees responsible for permit compliance must be regularly
trained or informed of any information pertinent to the proper operation and
maintenance of the facility and waste disposal. Training shall include topics such
as land application of wastes, proper operation and maintenance of the facility,
good housekeeping and material management practices, necessary record-keeping
requirements, and spill response and clean up. The permittee is responsible for
determining the appropriate training frequency for different levels of personnel and
the NMP shall identify periodic dates for such training.

Part V. Discharge Monitoring and Notification
Requirements
A. Notification of Discharges Resulting from Manure, Litter,
and Process Wastewater Storage, Handling, On-site
Transport and Application
If, for any reason, there is a discharge of pollutants to waters of the United States, the permittee
is required to make immediate oral notification within 24 hours to the permitting authority. The
permittee is also required to notify the permitting authority in writing at the address in Part I.E.4
of this permit within 5 working days of the discharge from the facility. In addition, the permittee
shall keep a copy of the notification submitted to the permitting authority together with the
other records required by this permit. The discharge notification shall include the following
information:
1. A description of the discharge and its cause, including a description of the flow path to
the receiving waterbody and an estimate of the flow and volume discharged.
2. The period of noncompliance, including exact dates and times, the anticipated time it
is expected to continue, and steps taken or planned to reduce, eliminate and prevent
recurrence of the discharge.

B. Monitoring Requirements for All Discharges from Retention
Structures
If any overflow or other discharge of pollutants occurs from a manure and/or wastewater
storage or retention structure, whether or not authorized by this permit, the permittee shall take
following actions:
1. All discharges shall be sampled and analyzed. Samples must, at a minimum, be
analyzed for the following parameters: total nitrogen, ammonia nitrogen phosphorus,
fecal coliform, 5-day biochemical oxygen demand (BOD5), total suspended solids, pH,
and temperature. The discharge must be analyzed in accordance with approved U.S.
Environmental Protection Agency methods for water analysis listed in 40 CFR part 136.

Appendix O: Sample Site-Specific NPDES General Permit
Part V. Discharge Monitoring and Notification Requirements

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NPDES Permit Writers’ Manual for CAFOs

2. Record an estimate of the volume of the release and the date and time.
3. Samples shall consist of grab samples collected from the over-flow or discharges
from the retention structure. A minimum of one sample shall be collected from the
initial discharge (within 30 minutes). The sample shall be collected and analyzed in
accordance with U.S. the U.S. Environmental Protection Agency approved methods for
water analysis listed in 40 CFR part 136. Samples collected shall be representative of the
monitored discharge. The discharge must be collected in accordance with approved U.S.
Environmental Protection Agency methods for water analysis listed in 40 CFR part 136.
4. If conditions are not safe for sampling, the permittee must provide documentation of
why samples could not be collected and analyzed. For example, the permittee may
be unable to collect samples during dangerous weather conditions (such as local
flooding, high winds, hurricane, tornadoes, electrical storms, and such). However,
once dangerous conditions have passed, the permittee shall collect a sample from the
retention structure (pond or lagoon) from which the discharge occurred.

C. General Inspection, Monitoring, and Record-Keeping
Requirements
The permittee shall inspect, monitor, and record the results of such inspection and monitoring in
accordance with Table V–A.
Table V-A. NPDES Large CAFO Permit Record-keeping Requirements
Parameter

Units

Frequency

Permit and Nutrient Management Plan
(Note: Required by the NPDES CAFO Regulation—applicable to all CAFOs)
The CAFO must maintain on-site a copy of the current
NPDES permit, including the permit authorization
notice. [SPECIFY MECHANISM TO IDENTIFY SITESPECIFIC TERMS]

N/A

Maintain at all times

Permit and Nutrient Management Plan
(Note: Required by the NPDES CAFO Regulation—applicable to all CAFOs)
The CAFO must maintain on-site a current-site specific
NMP that reflects existing operational characteristics.
The operation must also maintain on-site all necessary
records to document that the NMP is being properly
implemented with respect to manure and wastewater
generation, storage and handling, and land
application. In addition, records must be maintained
that the development and implementation of the
NMP is in accordance with the minimum practices
defined in 40 CFR part 122.42(e).

Appendix O: Sample Site-Specific NPDES General Permit
Part V. Discharge Monitoring and Notification Requirements

N/A

Maintain at all times

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NPDES Permit Writers’ Manual for CAFOs

Table V-A. NPDES Large CAFO Permit Record-keeping Requirements (continued)
Parameter

Units

Frequency

Soil and Manure/Wastewater Nutrient Analysis
(Note: Required by the CAFO ELG—applicable to Large CAFOs)
Analysis of manure, litter, and process wastewater to
determine nitrogen and phosphorus content.a
Analysis of soil in all fields where land application
activities are conducted to determine phosphorus
content.a

ppm
Pounds/ton

At least annually
after initial sampling

ppm

At least once every
5 years after initial
sampling

Operation and Maintenance (Note: Required by the CAFO ELG—applicable to Large CAFOs)
Visual inspection of all water lines

N/A

Dailyb

Documentation of depth of manure and process
wastewater in all liquid impoundments

Feet

Weekly

Documentation of all corrective actions taken.
Deficiencies not corrected within 30 days must
be accompanied by an explanation of the factors
preventing immediate correction.

N/A

As necessary

Documentation of animal mortality handling
practices

N/A

As necessary

Design documentation for all manure, litter, and wastewater storage structures including the
following information:
Once
• Volume for solids accumulation
Cubic yards/gallons
in the
• Design treatment volume
Cubic yards/gallons
permit term
• Total design storage volumec
Cubic yards/gallons
unless revised
• Days of storage capacity
Days
Documentation of all overflows from all manure and wastewater storage structures including:
(Note: Required by the NPDES Regulation—applicable to all CAFOs)
• Date and time of overflow
Month/day/year
Per event
• Estimated volume of overflow
Total gallons
Per event
• Analysis of overflow (as required by the
TBD
Per event
Permitting Authority)
Land Application (Note: Required by the CAFO ELG—applicable to Large CAFOs)
For each application event where manure, litter, or process wastewater is applied, documentation of
the following by field:
• Date of application
Month/day/year
Daily
• Method of application
N/A
Daily
• Weather conditions at the time of application
N/A
Daily
and for 24 hours prior to and following
application
• Total amount of nitrogen and phosphorus
Pounds/acre
Daily
appliedd

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Part VI. Discharge Monitoring and Notification Requirements

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NPDES Permit Writers’ Manual for CAFOs

Table V-A. NPDES Large CAFO Permit Record-keeping Requirements (continued)
Parameter

Units

Frequency

Documentation of the crop and expected yield for
each field

Bushel/acre

Seasonally

Documentation of the actual crop planted and actual
yield for each field

Bushel/acre

Seasonally

Documentation of test methods and sampling
protocols used to sample and analyze manure, litter,
and wastewater and soil.

N/A

Once in the permit
term unless revised

Documentation of the basis for the application
rates used for each field where manure, litter, or
wastewater is applied.

N/A

Once in the permit
term unless revised

Pounds/acre

Once in the permit
term unless revised

N/A

Seasonally

Documentation showing the total nitrogen and
phosphorus to be applied to each field including
nutrients from the application of manure, litter, and
wastewater and other sources
Documentation of manure application equipment
inspection

Manure Transfer
(Note: Required by the NPDES CAFO Regulation—applicable to Large CAFOs)
For all manure transfers the CAFO must maintain the following records:
• Date of transfer
N/A
• Name and address of recipient
N/A
• Approximate amount of manure, litter, or
Tons/gallons
wastewater transferred

As necessary
As necessary
As necessary

Notes:
a. For the specific analyses to be used, see the state nutrient management technical standard.
b. Visual inspections should take place daily during the course of normal operations. The completion of such
inspection should be documented in a manner appropriate to the operation. Some operations might wish to
maintain a daily log. Other operations might choose to make a weekly entry, when they update other weekly
records that required daily inspections have been completed.
c. Total design volume includes normal precipitation less evaporation on the surface of the structure for the storage
period, normal runoff from the production area for the storage period, 25-year, 24-hour precipitation on the
surface of the structure, 25-year, 24-hour runoff from the production area, and residual solids.
d. Including quantity/volume of manure, litter, or process wastewater applied and the basis for the rate of phosphorus
application.

Appendix O: Sample Site-Specific NPDES General Permit
Part V. Discharge Monitoring and Notification Requirements

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NPDES Permit Writers’ Manual for CAFOs

Part VI. Annual Reporting Requirements
A. The permittee must submit an annual report to the
permitting authority by the 31st of July of each year.
B. The annual report must include the following information:
1. The number and type of animals, whether in open confinement or housed under roof.
2. Estimated amount of total manure, litter, and process wastewater generated by the
CAFO in the previous 12 months (tons/gallons).
3. Estimated amount of total manure, litter, and process wastewater transferred to other
person by the CAFO in the previous 12 months (tons/gallons).
4. Total number of acres for land application covered by the NMP.
5. Total number of acres under control of the CAFO that were used for land application of
manure, litter, and process wastewater in the previous 12 months.
6. Summary of all manure, litter, and process wastewater discharges from the production
area that have occurred in the previous 12 months, including date, time, and
approximate volume.
7. A statement indicating whether the current version of the CAFO’s NMP was developed
or approved by a certified nutrient management planner.
8. Actual crops planted and actual yields for each field for the preceding 12 months.
9. Results of all samples of manure, litter or process wastewater for nitrogen and
phosphorus content for manure, litter and process wastewater that was land applied.
10. Results of calculations conducted in accordance with Part III.A.6.a of this permit.
11. Amount of manure, litter, and process wastewater applied to each field during the
preceding 12 months.
12. For rates of application:
i. The results of any soil testing for nitrogen and phosphorus conducted during the
preceding 12 months.
ii. The data used in calculations conducted in accordance with Part III.A.3.h of tis
permit.
iii. The amount of any supplemental fertilizer applied during the preceding 12 months.

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Part VI. Annual Reporting Requirements

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NPDES Permit Writers’ Manual for CAFOs

Part VII. Standard Permit Conditions
A. General Conditions
1. In accordance with the provisions of 40 CFR part 122.41 et. seq., this permit
incorporates by reference all conditions and requirements applicable to NPDES
Permits set forth in the Clean Water Act, as amended, (the Act) and all applicable
regulations.
2. The permittee must comply with all conditions of this permit. Any permit
noncompliance constitutes a violation of the Act and is grounds for enforcement
action; for permit termination, revocation, and reissuance; for denial of a permit
renewal application; and/or for requiring a permittee to apply for and obtain an
individual NPDES permit.
3. The permittee shall comply with effluent standards and prohibitions established under
section 307(a) of the Act for toxic pollutants within the time provided in the regulations
that establish those standards or prohibitions, even if the permit has not yet been
modified to incorporate the requirement.
4. This permit may be modified, revoked and reissued, or terminated for cause. The filing
of a request for a permit modification, revocation and reissuance, or termination, or
a notification of planned changes or anticipated noncompliance, does not stay any
permit condition.
5. The issuance of this permit does not convey any property rights of any sort, or any
exclusive privileges, nor does it authorize any injury to private property or any
invasion of personal rights, nor any infringement of federal, state/tribal or local laws or
regulations.
6. The permittee shall furnish to the permitting authority, within a reasonable time,
any information that the Director might request to determine whether cause exists
for modifying, revoking and reissuing, or terminating this permit, or to determine
compliance with this permit. The permittee shall also furnish to the permitting
authority, on request, copies of records required to be kept by this permit.
7. Nothing in this permit shall be construed to relieve the permittee from civil
or criminal penalties for noncompliance. Any false or materially misleading
representation or concealment of information required to be reported by the
provisions of the permit, the Act, or applicable regulations, which avoids or effectively
defeats the regulatory purpose of the permit may subject the permittee to criminal
enforcement pursuant to 18 U.S.C. 1001.
8. Nothing in this permit shall be construed to preclude the institution of any legal action
or relieve the permittee from any responsibilities, liabilities, or penalties established

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Part VII. Standard Permit Conditions

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NPDES Permit Writers’ Manual for CAFOs

pursuant to any applicable state/tribal law or regulation under authority preserved by
section 510 of the Act.
9. The provisions of this permit are severable, and if any provision of this permit or the
application of any provision of this permit to any circumstance, is held invalid, the
application of such provision to other circumstances, and the remainder of this permit,
shall not be affected thereby.
10. Bypass
a. Definitions
i. Bypass means the intentional diversion of waste streams from any portion of a
treatment facility.
ii. Severe property damage means substantial physical damage to property,
damage to the treatment facilities that causes them to become inoperable, or
substantial and permanent loss of natural resources that can reasonably be
expected to occur in the absence of a bypass. Severe property damage does not
mean economic loss caused by delays in production.
b. Bypass not exceeding limitations. The permittee may allow any bypass to occur that
does not cause effluent limitations to be exceeded but only if it also is for essential
maintenance to assure efficient operation. Those bypasses are not subject to
Parts VII.A.10.c. and 10.d. of this permit.
c. Notice
i. Anticipated bypass. If the permittee knows in advance of the need for a bypass,
it shall submit prior notice, if possible at least 10 days before the date of the
bypass.
ii. Unanticipated bypass. The permittee shall submit notice of unanticipated
bypass as required in Part VII.D.5. of this permit (24-hour notice).
d. Prohibitions of bypass.
i. Bypass is prohibited, and the permitting authority may take enforcement
action against a permittee for bypass, unless the following are true:
• Bypass was unavoidable to prevent loss of life, personal injury, or severe
property damage.
• There were no feasible alternatives to the bypass, such as the use of
auxiliary treatment facilities, retention of untreated wastes, or maintenance
during normal periods of equipment downtime. That condition is not
satisfied if adequate backup equipment should have been installed in
the exercise of reasonable engineering judgment to prevent a bypass that
occurred during normal periods of equipment downtime or preventive
maintenance.

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Part VII. Standard Permit Conditions

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NPDES Permit Writers’ Manual for CAFOs

• The permittee submitted notices as required under Part VII.A.10.c. of this
permit.
ii. The permitting authority may approve an anticipated bypass, after considering
its adverse effects, if the permitting authority determines that it will meet the
three conditions listed above in Part VII.A.10.d.(i) of this permit.
11. Upset
a. Definition. Upset means an exceptional incident in which there is unintentional
and temporary noncompliance with technology-based permit effluent limitations
because of factors beyond the reasonable control of the permittee. An upset does
not include noncompliance caused by operational error, improperly designed
treatment facilities, lack of preventive maintenance, or careless or improper
operation.
b. Effect of an upset. An upset constitutes an affirmative defense to an action brought
for noncompliance with such technology-based permit effluent limitations if the
requirements of Part VII.A.11.c. of this permit are met.
c. Conditions necessary for a demonstration of upset. A permittee who wishes to
establish the affirmative defense of upset shall demonstrate, through properly
signed, contemporaneous operating logs, or other relevant evidence of the
following:
i. An upset occurred and that the permittee can identify the cause(s) of the upset.
ii. The permitted facility was at the time being properly operated.
iii. The permittee submitted notice of the upset as required in Part VII.D.5 of this
permit (24-hour notice).
iv. The permittee complied with any remedial measures required under
Part VII.A.14 of this permit (duty to mitigate).
d. Burden of proof. In any enforcement proceeding, the permittee seeking to establish
the occurrence of an upset has the burden of proof.
12. Duty to reapply. If the permittee wishes to continue an activity regulated by this permit
after the expiration date of this permit, the permittee must apply for and obtain a new
permit.
13. Need to halt or reduce activity not a defense. It shall not be a defense for a permittee
in an enforcement action that it would have been necessary to halt or reduce the
permitted activity to maintain compliance with the conditions of this permit.
14. Duty to mitigate. The permittee shall take all reasonable steps to minimize or prevent
any discharge or sludge use or disposal in violation of this permit, which has a
reasonable likelihood of adversely affecting human health or the environment.

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Part VII. Standard Permit Conditions

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NPDES Permit Writers’ Manual for CAFOs

15. Inspection and entry. The permittee shall allow the permitting authority, or
an authorized representative (including an authorized contractor acting as a
representative of the permitting authority), upon presentation of credentials and other
documents as may be required by law, to do the following:
a. Enter the permittee’s premises where a regulated facility or activity is located or
conducted, or where records must be kept under the conditions of this permit
b. Have access to and copy, at reasonable times, any records that must be kept under
the conditions of this permit
c. Inspect at reasonable times any facilities, equipment (including monitoring and
control equipment), practices, or operations regulated or required under this
permit
d. Sample or monitor at reasonable times, for the purposes of assuring permit
compliance or as otherwise authorized by the Act, any substances or parameters at
any location.

B. Proper Operation and Maintenance
The permittee shall, at all times, properly operate and maintain all facilities and systems of
treatment and control (and related appurtenances) that are installed or used by the permittee
to achieve compliance with the conditions of this permit. Proper operation and maintenance
includes the operation of backup or auxiliary facilities or similar systems only when necessary to
achieve compliance with the conditions of the permit.

C. Monitoring and Records
1. Samples and measurements taken for the purpose of monitoring shall be
representative of the monitored activity.
2. The permittee shall retain records of all monitoring information, including all
calibration and maintenance records and all original strip chart recordings for
continuous monitoring instrumentation, copies of all reports required by this permit,
and records of all data used to complete the application for this permit, for a period of
at least 5 years from the date of the sample, measurement, report, or application. That
period may be extended by request of the permitting authority at any time.
3. Records of monitoring information shall include the following:
a. The date, exact place, and time of sampling or measurements.
b. The individual(s) who performed the sampling or measurements.
c. The date(s) analyses were performed.
d. The individual(s) who performed the analyses.

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Part VII. Standard Permit Conditions

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NPDES Permit Writers’ Manual for CAFOs

e. The analytical techniques or methods used.
f. The results of such analyses.
4. The permittee shall follow the following monitoring procedures:
a. Any required monitoring must be conducted according to test procedures
approved under 40 CFR part 136, unless other test procedures have been specified
in this permit or approved by the permitting authority.
b. The permittee shall calibrate and perform maintenance procedures on all
monitoring and analytical instruments at intervals frequent enough to ensure
accuracy of measurements and shall maintain appropriate records of such
activities.
c. An adequate analytical quality control program, including the analyses of
sufficient standards, spikes, and duplicate samples to ensure the accuracy of all
required analytical results shall be maintained by the permittee or designated
commercial laboratory.
5. Monitoring reports. Monitoring results shall be reported at the intervals specified
elsewhere in this permit.
a. Monitoring results must be reported on a Discharge Monitoring Report (DMR) or
forms provided or specified by the permitting authority for reporting results of
monitoring of sludge use or disposal practices.
b. If the permittee monitors any pollutant more frequently than required by the
permit using test procedures approved under 40 CFR part 136 or, in the case of
sludge use or disposal, approved under 40 CFR part 136 unless otherwise specified
in 40 CFR part 503, or as specified in the permit, the results of this monitoring shall
be included in the calculation and reporting of the data submitted in the DMR or
sludge reporting form specified by the permitting authority.
c. Calculations for all limitations which require averaging of measurements shall
utilize an arithmetic mean unless otherwise specified by the permitting authority
in the permit.

D. Reporting Requirements
1. The permittee shall give notice to the permitting authority as soon as possible of any
planned physical alterations or additions to the permitted facility. Notice is required
only when any of the following are true:
a. The alteration or addition to a permitted facility may meet one of the criteria for
determining whether a facility is a new source in 40 CFR part 122.29(b).
b. The alteration or addition could significantly change the nature or increase
the quantity of pollutants discharged. The notification applies to pollutants

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Part VII. Standard Permit Conditions

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NPDES Permit Writers’ Manual for CAFOs

that are subject neither to effluent limitations in the permit, nor to notification
requirements under 40 CFR part 122.42(a)(1).
c. The alteration or addition results in a significant change in the permittee’s manure
use or disposal practices, and such alteration, addition, or change could justify the
application of permit conditions that are different from or absent in the existing
permit, including notification of additional use or disposal sites not reported
during the permit application process or not reported pursuant to an NMP.
2. The permittee shall give advance notice to the permitting authority of any
planned physical alterations or additions or changes in activity that could result in
noncompliance with requirements in this permit.
3. This permit is not transferable to any person except after notice to permitting authority.
The permitting authority may require modification or revocation and reissuance of the
permit to change the name or the permittee and incorporate such other requirements
as might be necessary under the Act.
4. Reports of compliance or noncompliance with, or any progress reports on, interim
and final requirements contained in any compliance schedule of this permit shall be
submitted no later than 14 days following each scheduled date.
5. The permittee shall report any noncompliance that could endanger human health or
the environment. Any information must be provided orally to the permitting authority
within 24 hours from the time that the permittee becomes aware of the circumstances.
A written submission shall also be provided to the permitting authority within 5 days
of the time the permittee becomes aware of the circumstances. The report shall
contain the following information:
a. A description of the noncompliance and its cause
b. The period of noncompliance, including exact dates and times, and if the
noncompliance has not been corrected, the anticipated time it is expected to
continue
c. Steps taken or planned to reduce, eliminate, and prevent recurrence of the
noncompliance
6. The following shall be included as information, which must be reported within
24 hours:
a. Any unanticipated bypass that exceeds any effluent limitation in the permit
b. Any upset that exceeds any effluent limitation in the permit
c. Violation of a maximum daily discharge limitation for any of the pollutants listed
by the permitting authority in the permit to be reported within 24 hours

The permitting authority may waive the written report on a case-by-case basis for
reports under the above if the oral report has been received within 24 hours.

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Part VII. Standard Permit Conditions

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NPDES Permit Writers’ Manual for CAFOs

7. The permittee shall report all instances of noncompliance not reported under above
and of this section, at the time monitoring reports are submitted. The reports shall
contain the information listed in Part VII.D.6 of this permit.
8. Where the permittee becomes aware that it failed to submit any relevant facts in a
permit application, or submitted incorrect information in a permit application or in
any report to the permitting authority, the permittee shall promptly submit such facts
or information to the permitting authority.

E. Signatory requirements
All applications, reports, or information submitted to the permitting authority shall be signed and
certified consistent with 40 CFR part 122.22:
1. All notices of intent shall be signed as follows:
a. For a corporation: By a responsible corporate officer. For the purpose of this
section, a responsible corporate officer means either of the following:
i. A president, secretary, treasurer, or vice-president of the corporation in charge
of a principal business function, or any other person who performs similar
policy or decision-making functions for the corporation.
ii. The manager of one or more manufacturing, production, or operating facilities,
provided, the manager is authorized to make management decisions that
govern the operation of the regulated facility including having the explicit
or implicit duty of making major capital investment recommendations, and
initiating and directing other comprehensive measures to assure long-term
environmental compliance with environmental laws and regulations; the
manager can ensure that the necessary systems are established or actions
taken to gather complete and accurate information for permit application
requirements; and where authority to sign documents has been assigned or
delegated to the manager in accordance with corporate procedures.
iii. For a partnership or sole proprietorship: By a general partner for a partnership
or the proprietor, respectively.
2. All reports required by the permit and other information requested by the U.S.
Environmental Protection Agency shall be signed by a person described above or
by a duly authorized representative of that person. A person is a duly authorized
representative only if the following are true:
a. The authorization is made in writing by a person described above.
b. The authorization specifies either an individual or a position having responsibility
for the overall operation of the regulated facility or activity, such as the position
of plant manager, operator of a well or a well field, superintendent, position
of equivalent responsibility, or any individual or position having overall
responsibility for environmental matters for the company. A duly authorized

Appendix O: Sample Site-Specific NPDES General Permit
Part VII. Standard Permit Conditions

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NPDES Permit Writers’ Manual for CAFOs

representative may thus be either a named individual or an individual occupying a
named position.
c. The written authorization is submitted to the U.S. Environmental Protection
Agency.

F. Availability of Reports
Any information submitted pursuant to this permit may be claimed as confidential by the
submitter. If no claim is made at the time of submission, information may be made available to
the public without further notice.

G. Penalties for Violations of Permit Conditions
1. Criminal Penalties:
a. Negligent violations: The Act provides that any person who negligently violates
section 301, 302, 306, 307, 308, 318, or 405 of the Act or any condition or limitation
implementing those provisions in a permit issued under section 402 is subject
to a fine of not less than $2,750 nor more than $27,500 per day of violation, or by
imprisonment for not more than one year, or both.
b. Knowing violations: The Act provides that any person who knowingly violates
sections 301, 302, 306, 307, 308, 318, or 405 of the Act or any permit conditions
implementing those provisions is subject to a fine of not less than $5,500 nor more
than $55,000 per day of violation, or by imprisonment for not more than 3 years, or
both.
c. Knowing endangerment: The Act provides that any person who knowingly violates
sections 301, 302, 303, 306, 307, 308, 318, or 405 of the Act or permit conditions
implementing those provisions and who knows at that time that he or she is
placing another person in imminent danger of death or serious bodily injury is
subject to a fine of not more than $275,000, or by imprisonment for not more than
15 years, or both.
d. False statements: The Act provides that any person who knowingly makes any
false material statement, representation, or certification in any application, record,
report, plan, or other document filed or required to be maintained under the Act
or who knowingly falsifies, tampers with, or renders inaccurate, any monitoring
device or method required to be maintained under the Act, shall upon conviction,
be punished by a fine of not more than $11,000, or by imprisonment for not more
than 2 years, or by both. If a conviction of a person is for a violation committed
after a first conviction of such person under this paragraph, punishment shall be
by a fine of not more than $22,000 per day of violation, or by imprisonment of not
more than 4 years, or by both. [See section 309(c)4 of the Clean Water Act.]

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Part VII. Standard Permit Conditions

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NPDES Permit Writers’ Manual for CAFOs

2. Civil penalties: The Act provides that any person who violates a permit condition
implementing sections 301, 302, 306, 307, 308, 318, or 405 of the Act is subject to a civil
penalty not to exceed $27,500 per day for each violation. [See section 309(d).]
3. Administrative penalties: The Act provides that the Administrator may assess a Class I
or Class II administrative penalty if the Administrator finds that a person has violated
sections 301, 302, 306, 307, 308, 318, or 405 of the Act or a permit condition or limitation
implementing these provisions, as follows [See section 309(g).]:
a. Class I penalty: Not to exceed $11,000 per violation nor shall the maximum amount
exceed $27,500.
b. Class II penalty: Not to exceed $11,000 per day for each day during which the
violation continues nor shall the maximum amount exceed $137,500.

Part VIII. Definitions
Animal feeding operation means a lot or facility (other than an aquatic animal production
facility) where the following conditions are met: (i) animals (other than aquatic animals) have
been, are, or will be stabled or confined and fed or maintained for a total of 45 days or more in
any 12-month period, and (ii) crops, vegetation, forage growth, or post-harvest residues are not
sustained in the normal growing season over any portion of the lot or facility.
Application means the EPA standard national forms for seeking coverage under for an NPDES
permit, including any additions, revisions or modifications to the forms; or forms approved by
EPA for use in approved states, including any approved modifications or revisions [e.g. for NPDES
general permits, a written NOI pursuant to 40 CFR part 122.28; for NPDES individual permits,
Form 1 and 2B pursuant to 40 CFR part 122.1(d)].
Concentrated animal feeding operation (CAFO) means an AFO that is defined as a Large CAFO
or Medium CAFO by 40 CFR parts 122.23 (4) and (6), or that is designated as a CAFO.
Fecal coliform means the bacterial count (Parameter 1 at 40 CFR part 136.3 in Table 1A), which
also cites the approved methods of analysis.
Grab sample means a sample that is taken from a wastestream on a one-time basis without
consideration of the flow rate of the wastestream and without consideration of time.
Land application means the application of manure, litter, or process wastewater onto or
incorporated into the soil.
Land application area means land under the control of a CAFO owner or operator, whether it is
owned, rented, or leased, to which manure, litter, or process wastewater from the production area
is or could be applied.

Appendix O: Sample Site-Specific NPDES General Permit
Part VIII. Definitions

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NPDES Permit Writers’ Manual for CAFOs

Large CAFO means an AFO that stables or confines as many as or more than the numbers of
animals specified in any of the following categories: (i) 700 mature dairy cattle, whether milked
or dry; (ii)1,000 veal calves; (iii)1,000 cattle other than mature dairy cows or veal calves. Cattle
includes but is not limited to heifers, steers, bulls and cow/calf pairs; (iv) 2,500 swine each
weighing 55 pounds or more; (v)10,000 swine each weighing less than 55 pounds; (vi) 500 horses;
(vii) 10,000 sheep or lambs; (viii) 55,000 turkeys; (ix) 30,000 laying hens or broilers, if the AFO uses
a liquid manure handling system; (x)125,000 chickens (other than laying hens), if the AFO uses
other than a liquid manure handling system; (xi) 82,000 laying hens, if the AFO uses other than
a liquid manure handling system; (xii) 30,000 ducks (if the AFO uses other than a liquid manure
handling system); or (xiii) 5,000 ducks (if the AFO uses a liquid manure handling system).
Liquid manure handling system means a system that collects and transports or moves waste
material with the use of water, such as in washing pens and flushing confinement facilities. That
includes the use of water impoundments for manure or wastewater treatment.
Manure is defined to include manure, litter, bedding, compost and raw materials or other
materials commingled with manure or set aside for land application or other use.
Medium CAFO means any AFO that stables or confines as many or more than the numbers of
animals specified in any of the following categories: (i) 200 to 699 mature dairy cattle, whether
milked or dry cows; (ii) 300 to 999 veal calves; (iii) 300 to 999 cattle other than mature dairy cows
or veal calves. Cattle includes but is not limited to heifers, steers, bulls and cow/calf pairs; (iv) 750
to 2,499 swine each weighing 55 pounds or more; (v) 3,000 to 9,999 swine each weighing less
than 55 pounds; (vi) 150 to 499 horses, (vii) 3,000 to 9,999 sheep or lambs, (viii) 16,500 to 54,999
turkeys, (ix) 9,000 to 29,999 laying hens or broilers, if the AFO uses a liquid manure handling
system; (x) 37,500 to 124,999 chickens (other than laying hens), if the AFO uses other than a liquid
manure handling system; (xi) 25,000 to 81,999 laying hens, if the AFO uses other than a liquid
manure handling system; (xii) 10,000 to 29,999 ducks (if the AFO uses other than a liquid manure
handling system); or (xiii) 1,500 to 4,999 ducks (if the AFO uses a liquid manure handling system)
and either one of the following conditions are met (a) pollutants are discharged into waters of the
United States through a man-made ditch, flushing system, or other similar man-made device; or
(b) pollutants are discharged directly into waters of the United States that originate outside and
pass over, across, or through the facility or otherwise come into direct contact with the animals
confined in the operation.
Notice of Intent (NOI) is a form submitted by the owner/operator applying for coverage under
a general permit. It requires the applicant to submit the information necessary for adequate
program implementation, including, at a minimum, the legal name and address of the owner or
operator, the facility name and address, type of facility or discharges, and the receiving stream(s).
40 CFR § 128.28(b)(2)(ii)
Process wastewater means water directly or indirectly used in the operation of the CAFO for any
or all of the following: spillage or overflow from animal or poultry watering systems; washing,
cleaning, or flushing pens, barns, manure pits, or other AFO facilities; direct contact swimming,

Appendix O: Sample Site-Specific NPDES General Permit
Part VIII. Definitions

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NPDES Permit Writers’ Manual for CAFOs

washing, or spray cooling of animals; or dust control. Process wastewater also includes any
water that comes into contact with or is a constituent of raw materials, products, or by-products
including manure, litter, feed, milk, eggs, or bedding.
Production area means that part of an AFO that includes the animal confinement area,
the manure storage area, the raw materials storage area, and the waste containment areas.
The animal containment area includes but is not limited to open lots, housed lots, feedlots,
confinement houses, stall barns, free stall barns, milk rooms, milking centers, cowyards,
barnyards, medication pens, walkers, animal walkways, and stables. The manure storage area
includes but is not limited to lagoons, runoff ponds, storage sheds, stockpiles, under house
or pit storages, liquid impoundments, static piles, and composting piles. The raw materials
storage area includes but is not limited to feed silos, silage bunkers, and bedding materials. The
waste containment area includes but is not limited to settling basins, and areas within berms
and diversions that separate uncontaminated stormwater. Also included in the definition of
production area is any egg washing or egg processing facility, and any area used in the storage,
handling, treatment, or disposal of mortalities.
Small CAFO means an AFO that is designated as a CAFO and is not a Medium CAFO.
Setback means a specified distance from waters of the United States or potential conduits to
waters of the United States where manure, litter, and process wastewater may not be land applied.
Examples of conduits to surface waters include open tile line intake structures, sinkholes, and
agricultural well heads.
The Act means Federal Water Pollution Control Act as amended, also known as the Clean Water
Act as amended, found at 33 U.S.C. 1251 et seq.
Vegetated buffer means a narrow, permanent strip of dense perennial vegetation established
parallel to the contours of and perpendicular to the dominant slope of the field for the purposes
of slowing water runoff, enhancing water infiltration, and minimizing the risk of any potential
nutrients or pollutants from leaving the field and reaching waters of the United States.
Waters of the United States means (1) all waters that are used, were used in the past, or might be
susceptible to use in interstate or foreign commerce, including all waters that are subject to the
ebb and flow of the tide; (2) all interstate waters, including interstate wetlands; (3) all other waters
such as intrastate lakes, rivers, and streams (including intermittent streams), mudflats, sandflats,
wetlands, sloughs, prairie potholes, wet meadows, playa lakes, or natural ponds the use,
degradation, or destruction of which would affect or could affect interstate or foreign commerce
including any such waters: (a) that are or could be used by interstate or foreign travelers for
recreational or other purposes; from which fish or shellfish are or could be taken and sold in
interstate or foreign commerce; or that are or could be used for industrial purposes by industries
in interstate commerce; (4) all impoundments of waters otherwise defined as waters of the United
States; (5) tributaries of waters identified in (1) through (4) of this definition; (6) the territorial sea;
and (7) wetlands adjacent to waters (other than waters that are themselves wetlands) identified in
items (1) through (6) of this definition.

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Part VIII. Definitions

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NPDES Permit Writers’ Manual for CAFOs

Appendix A.
(Insert Form 2B/Notice of Intent or Appropriate State Form)

Appendix O: Sample Site-Specific NPDES General Permit
Appendix A

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NPDES Permit Writers’ Manual for CAFOs

Appendix B.

Sample Technical Standard
for Nutrient Management

While this sample technical standard is adapted from Iowa state publications, it does not
constitute Iowa’s technical standard for nutrient management. This documentation has not
been identified by the Iowa State Director as required by 40 C.F.R. 123.36 nor has EPA
reviewed these documents for consistency with the requirements of 40 C.F.R. 412.4(c)(2).
EPA is circulating this technical standard to demonstrate how the terms of the nutrient management
plan depend on technical information that would be found in a technical standard. Some of the
original documents have been modified to better illustrate the relationship between techincal
standards and terms. Circulation of the sample technical standards herein does not constitute an
endorsement of this technical documentation as an adequate technical standard for Iowa.
This sample is intended for educational purposes only and does not create or remove any legal
rights or requirements upon any member of the public, States or any other Federal agency.

Appendix O: Sample Site-Specific NPDES General Permit
Appendix B. State Technical Standards for Nutrient Management

Introduction and Instructions for the

Manure Management Plan Form

O-45

Iowa law requires certain confinement feeding operations to develop and obtain Department of Natural
Resources (DNR) approval of a manure management plan (MMP), to apply manure in accordance with
the plan, to submit annual updates of the manure management plan, to pay an annual compliance fee and
to provide copies of the manure management plan to the counties where the operation is located and where
manure is applied. Manure management plans submitted to the DNR must use the attached forms.
Submit one copy of the MMP to the DNR, two if you are applying for a construction permit. Additionally,
submit one copy to the county where the facility is located, one to each county where manure will be
applied, and keep a copy within 30 miles of the operation. It is recommended that one copy be kept for
your manure applicator.
These forms are not intended for use if manure is being sold. Plans involving the sale of manure should be
developed in accordance with the requirements of DNR rules 567 Iowa Administrative Code 65.17(2).
These rules are found in Appendix A.9 of these forms. Forms can be found on the DNR website at
http://www.state.ia.us/epd/wastewtr/feedlot/manure.htm.
Who Needs to Submit a Plan and Annual Updates?
•

Owners of confinement animal feeding operations constructed or expanded after May 31, 1985 (unless the
operation is a small animal feeding operation 1 );

•

If you are constructing a manure storage structure or a confinement building – you must submit an original
manure management plan (unless the operation is a small animal feeding operation 1);

•

Owners of out-of-state confinement operations that apply manure in Iowa (unless the operation is a small
animal feeding operation 1).

Instructions for Use of These Forms
•

Make additional copies of pages 2 and 3 as needed.

•

A copy of the manure management plan and attachments listed on the following page must be provided to the
county where the facility is located and each county where manure is applied. Submit a signed copy of the
Verification of County Receipt for MMP to the DNR for each county involved. Use the form for nonpermitted sites Verification of County Receipt (Form 542-8046) Verification of County Receipt (Form 5428046) OR if a construction permit is required, use the Construction Application Package and use fee forms
for construction permit sites (Form 542-1428).

•

In addition to the required forms, information indicated on the following page must be submitted to DNR and
maintained as part of the current manure management plan.
1.

Small animal feeding operation: an animal feeding operation which has an animal unit capacity of 500 au or less.

updated 8/04 to include P Index; rev. 3/06 added Col. 11 to p. 3, rev.2/07 added existing operation, new owner

1

542-4000

O-46
SECTION A:
Attachments to be submitted to the county and maintained with the current MMP within thirty miles of
the site (in addition to required forms): These items are not required to be submitted to DNR.
•
•
•
•

A plat map which shows the location of the confinement feeding operation and of all fields being used for
manure application;
Aerial photos (available from the county Farm Services Agency office) or similar photos of all fields being
used for manure application. For each field, mark the field boundaries, areas not available or unsuitable for
manure application, and areas where specific restrictions on manure application apply;
Information documenting the optimum yields calculated for the manure application fields (if required – see
footnote “h”);
Operations using irrigation to apply manure must provide information indicating how they will comply with
applicable restrictions and requirements, and any additional methods or practices that will be used to reduce
potential odors.

SECTION B:
Attachments to be submitted to DNR (in addition to required forms):
With Annual Updates
• The Annual Compliance Fee form – Annual Compliance Fee (Form 542-8064) rev. 3/06 and a check for the
amount due ($0.15 per animal unit);
• MMP Short Form 2 (Form 542-8162)
With an Original MMP (new construction or expansion) and with an Original P Index-Based MMP
• A plat map which shows the location of the confinement operation.
• Written manure application agreements for all fields identified in the plan that are not owned or rented for
crop production purposes by the owner of the confinement feeding operation;
• Manure sampling results, if sample results were used to determine the manure’s nutrient content for this plan;
• When the P index is required, the MMP must include the NRCS P index “detailed report” from the Iowa P
index calculator (available at http://www.ia.nrcs.usda.gov/) with a P index for each field and a document (e.g.
RUSLE2 profile erosion calculation record) indicating the inputs and results of RUSLE2 for each field in the
plan. The “detailed report” should be submitted with this form once every 4 years as the update.
• For permitted sites only: The aerial photos of the manure application fields must be submitted for permitted
sites.
• The Filing Fee form [for facilities filing an MMP for construction, expansion or modification or filing an
original (first-time) MMP] and a check for the $250 filing fee and the indemnity fee if required:
(No indemnity fee applies if the operation was constructed or expanded prior to May 31, 1995 and no
construction permit was required.)
• For non-permitted sites: Indemnity fee and MMP filing fee and form (Form 542-4021) rev 3/06.
• For permitted sites - please follow instructions in the Construction Permit Application form (Form 5424021) rev. 6/03).
• Verification form of county receipt for non-permitted sites, OR if applying for a construction permit,
follow the instructions on the application (Form 542-4021).
•

DNR may request submittal of the attachments listed in Section A that are maintained with the current MMP.

2

Plan Updates & Recordkeeping

O-47

Prior to making changes in an operation’s manure management practices, the operation must update the plan to
show the proposed changes. Updates that occur after the submittal of the plan should be maintained on site and
indicated with the next annual update to DNR and the counties.
Records of manure application must be maintained within thirty miles of the confinement site, and must be
available for DNR inspection. For a list of record keeping requirements, see 65.17(13) of appendix A9. Records
must be maintained for five years after the year of manure application or for the length of the crop rotation,
whichever is greater.
Assistance
Assistance in developing a manure management plan may be available from a number of sources, including
private consultants, Iowa State University Extension, and USDA’s Natural Resources Conservation Service.
Some of these sources will prepare a complete plan for an operation, while others will only provide general
assistance. Contact your county extension or NRCS office to determine the assistance they will provide, as well
as to obtain a list of consultants who will prepare plans. If you have specific questions about the Manure
Management Plan forms, contact your regional DNR field office. See attached map for contact information and
to determine the appropriate office.
Mail Plan and Attachments
Please mail the plan, attachments and annual updates to the appropriate Iowa Department of Natural Resources
field office (See map below). If submitting a construction permit application, follow instructions on the
application form (Form 542-1428). Questions on permits? Please call 515-281-8941.
IOWA DEPARTMENT OF NATURAL RESOURCES
Environmental Services Division Field Office Locations

DNR Environmental Services Division

Example of Legal Description for Facility
Please refer to the example on the
right when describing the location of
your operation on Page 1. This
property is located in Washington
Township, Polk County.

3

Field Office #1
909 West Main, Ste 4
Manchester, IA 52057
563-927-2640

Field Office #2
th
2300 15 St SW
Mason City, IA 50401
641-424-4073

Field Office #3
1900 N. Grand Ave.
Spencer, IA 51301
712-262-4177

Field Office #4
1401 Sunnyside Lane
Atlantic, IA 50022
712-243-1934

Field Office #5
401 SW 7th, Ste I
Des Moines, IA 50309
515-725-0268

Field Office #6
1023 W. Madison
Washington, IA 52353
319-653-2135

O-48

Manure Management Plan Form

Animal Feeding Operation Information

Page 1

Instructions: Complete this form for your animal feeding operation. Footnotes are provided on page 4.
The information within this form, and the attachments, describes my animal feeding operation, my manure storage and handling system, and
my planned manure management system. I (we) will manage the manure, and the nutrients it contains, as described within this manure
management plan (MMP) and any revisions of the plan, individual field information, and field summary sheet, and in accordance with current
rules and regulations. Deviations permitted by Iowa law will be documented and maintained in my records.

Signed:

(Signature)

Date:

(Print name)

Name of operation:

Facility ID No. __ __ __ __ __

Location of the operation*:

(911 Address)
(Town)

(State)

_____ ¼ of the _____ ¼ of Sec _____ T_____ R____
(¼ ¼ )

(¼)

(Section)

(Zip Code)

____________________

(Tier & Range)

(Township Name)

Owner and Contacts of the animal feeding operation:
Owner
Address
Email address (optional)

________________
(County)

Phone
Cell phone (optional)

Contact person (if different than owner)
Address

Phone

Email address (optional)

Cell phone (optional)

Contract Company (if applicable)

Phone

Address
This manure management plan is for: (check one)
existing operation, not expanding

existing operation, expanding

Construction and Expansion Dates:

existing operation, new owner

new operation

date of initial construction
and date(s) of all expansion(s)

Table 1. Information about livestock production and manure management system
1

Animal Type/
Production phase a

2

Max. Number
of Animals
Confined (head)

3

Manure Storage Structure b

Estimate of Annual Animal Production f:

4

5

Nc

P2O5 c

lb/1000 gal or lb/ton

6

gal/space/day
or
ton/space/year d

animals/year

Total Gallons
Total Tons

Source of Nutrient Content Data (columns 4, 5): standard tables, analysis of manure samples, other:
* An example of a legal description is available on page 3 of the Introduction and Instructions.
4

7

Days/yr
Facility
Occupied

8

Annual
Manure Produced e
(gal or tons)

O-49

Manure Management Plan Form

Determining Maximum Allowable Manure Application Rates
Page 2
Instructions: Complete a worksheet for each unique combination of the following factors (crop rotation, optimum crop

yield, manure nutrient concentration, remaining crop N need, method of application) that occurs at this operation. Footnotes
are given on pages 4, 5 and 6.

Management Identification (Mgt ID)g:
(identify this application scenario by letter)

Method used to determine optimum yield h:
Method of Application i:
If spray irrigation is used, identify method j:

Timing of Application:
Application Loss Factor i:

Table 2. Manure Nutrient Concentration

Table 3. Crop Usage Rates p

Manure Nutrient Content (lbs/1000gal or lbs/ton)
Manure Storage Structure(s) k
Total N
P2O5
st
l
nd
% 2 year
% TN available 1 year
% 3rd year
Available N 1st yearm
2nd year n
3rd year o

(lbs/bu or lbs/ton)
Corn
Soybean
Alfalfa

N
3.8
50

P2O5
0.375
0.8
12.5

* Use blank space above to add crop not listed.

Table 4. Calculations for rate based on nitrogen (always required).
1

Applying Manure For (crop to be grown)q

2

Optimum Crop Yield h

3
4

bu or ton/acre

P2O5 removed with crop by harvest
Crop N utilization

r

lb/acre

s

lb/acre

5a Legume N credit
5b Commercial N planned u
t

5c Manure N carryover credit
6
7
8

lb/acre
lb/acre
v

lb/acre

Remaining crop N need w

lb/acre

Manure rate to supply remaining N
P2O5 applied with N-based rate

x

gal/acre or ton/acre

y

lb/acre

Table 5. Calculations for rate based on phosphorus (fill out only if P-based rates are planned)
9

Commercial P2O5 planned z

lb/acre

10 Manure rate to supply P removal
11 Manure rate for P based plan

aa

gal/acre or ton/acre

bb

gal/acre or ton/acre

12 Manure N applied with P-based plan

cc

lb/acre

Table 6. Application rates that will be carried over to page 3.
13

Planned Manure Application Rate

dd

gal/acre or ton/acre

5

Manure Management Plan Form

Field
Designationee

1

2

3

4

5

6

6

Total acres available for manure application

P
Index
Value ii

7

(Y/N) jj

HEL

8

10

gal or
tons/acre

Total tons that could be applied

k

gal or
ton/fieldk

Planned
Application

9

Total gallons that could be applied

Own, rent, or
Acres
agreement
Field Location
Mgt Planned receiving (include length of
___ ¼ of the ___1/4 Sec ___ T____ R____
ff
Crop manure gg agreement) hh
Township Name _____________ County Name ____________ ID

Crop Year(s):

(Yes or
No)

Correct
Soils
Test for
P ll

11

Year by Year Manure Management Plan Summary
Page 3
Instructions: Complete this form for each of the next four growing seasons, to demonstrate sufficient land base to apply manure over multiple crop years.
If this page is identical for multiple years (e.g. every other year), submit only once for the identical years, and indicate which years the form represents.
Footnotes are given on page 6.

O-50

Manure Management Plan Footnotes

a

O-51

Page 4

Complete Appendix B1 Worksheet if a manure storage structure receives manure from several animal production phases and the
manure and nitrogen production values given in Appendices A1 and A2 do not adequately represent the operation (such as with a
farrow-to-finish swine operation where half the pigs produced are sold as feeders and the remainder held for finishing).
b

For example, indoor or outdoor formed storage, earthen basin, or anaerobic lagoon; to simplify calculations similar manure storage
structures that contain manure with essentially the same nutrient concentrations may be grouped together (for example, the manure
storage structures for a 3-building finishing unit with below-building pits could be identified as “3 below-building finishing pits”).
c

From standard tables (Appendix A4), your own samples, or other sources – identify source in space provided below Table 1 on page 1.
If your own samples are used, DNR requires submittal of laboratory reports supporting manure concentrations. If your own samples are
used, the results may need to be converted from parts per million (ppm) to pounds/1000 gallons. The formula for making this
conversion is: N or P2O5 concentration (lb/1000 gal) = N or P2O5 concentration in parts per million (ppm) X 0.00834. For solid manure
the conversion is: N or P2O5 concentration (lb/ton) = N or P2O5 concentration in parts per million (ppm) X 0.002. If measured volume
or weight of manure is used in the plan, actual N and P2O5 concentrations must also be used.
d

From Appendix A1; adjust values if operation has data justifying use of different volumes or weights (e.g., operation uses large
volume of clean up water, and thus its manure production volume per animal space is higher than that given in table). If actual volumes
or weights are used, DNR may require submittal of supporting data. If actual manure N and P 2O5 concentrations are used in the plan,
measured volume or weight must also be used.
e

Annual manure produced (liquid manure) = maximum number of animals confined (column 2) multiplied by (x) gal/space/day
(column 6) x days/ year building occupied (column 7). Annual manure produced (solid manure) = maximum number of animals
confined (column 2) x tons/space/year (column 6).
f

Estimated Annual Animal Production = Maximum number of animals confined (column 2 of Table 1) x production cycles per year. If
operation has no production cycles (e.g. sows) state only total maximum number confined.
g

Use the management ID to identify each unique combination of the following factors (crop rotation, optimum crop yields, manure
nutrient concentration, remaining crop N need, method of application) that occur. The idea behind the management ID is to group fields
with identical management on the same page 2, to avoid the redundancy of doing the exact same calculations for multiple fields.
For example, if 8 fields in the plan are in a corn/bean rotation with yields of 160 and 50 bu/acre and all will receive injected manure
with the same nutrient concentration and availability, then page two would only need to be filled out once for the 8 fields and the
management ID (e.g. “A”) would represent all 8 fields. The same management ID could be used to describe these fields even if they
were in different phases of the crop rotation (i.e. some are in corn and some in beans each year).
h
•
•
•
•
•

Yields can be used from any of the following:
USDA Iowa ag statistics county yield averages
Multi-peril insurance proven yields
USDA Farm Service Agency proven yields
Individual farm proven yields
Soil survey interpretation records

Documentation of the information used to determine optimum yields must kept with the plan (DNR may require submittal of yield

documentation). Documentation may include copies of historical farm yield records, soil survey maps and average yields for the soils
found, FSA yield data, etc... If Iowa Ag Statistics county average yields, Appendix A8, are used, documentation is not required to
determine optimum yields for corn and soybean crops. The optimum yield for each crop may be set equal to either the average of the
last 5-year county yields plus 10 percent or the average of the highest 4 out of the last 5-year county average. If crops other than corn or
soybeans are grown, Iowa Ag Statistics yield data for those crops will need to be obtained and optimum yield levels calculated (both the
yield data and the calculations should be kept with the plan). If proven yield methods are used to determine optimum yields, the
Appendix B2 Worksheet should be used to calculate the optimum yields.
i

Use list of application methods and application loss factors provided in Appendix A7. If methods other than those listed in Appendix
A7 are used, identify the methods and the nitrogen loss factors for those methods.

j

Use of spray irrigation for manure application: Iowa law includes a number of requirements and restrictions on applying manure
through spray irrigation. If spray irrigation is being used, the plan should identify the actions the operation will take to ensure
compliance with these requirements and restrictions. In addition, the plan should identify any additional methods or practices the
operation will use to reduce potential odor, if any additional methods will be used.
k

From Table 1 column 3.
7

O-52
l

Manure Management Plan Footnotes

Page 5

Recent research by Iowa State University indicates 100 percent of the nitrogen contained in liquid manure from confinement swine
operations is available for plant use in the first year after application. Prior research indicates this may not be the case for liquid manure
from other animal species or for solid (dry) manure from confinement operations. A manure management plan may be developed based
on the assumption that less than 100 percent of the nitrogen remaining in the manure after deducting application losses will be available
for plant use in the first crop year after manure application. However, for planning purposes all nitrogen not considered available in the
first crop year must be accounted for in subsequent crop years, and must be considered in determining allowable nitrogen applications
(from all sources) during those years. Suggested availability values are: liquid swine manure – 100% in 1st crop year; other liquid
manure – 75%, 15%, and 10% in 1st, 2nd, & 3rd crop years respectively; solid manure – 60-75% in 1st crop year, remainder split between
2nd and 3rd years.
m

1st year available N = Total N x Application loss factor x Percentage of TN available in the first year (e.g. for 95% N available in first
year multiply by 0.95), Appendix B3 can be used to make the calculation.
n

2nd year available N = Total N x Application loss factor x Percentage of TN available in the second year. Appendix B3 can be used to
make the calculation.

o

3rd year available N = Total N x Application loss factor x Percentage of TN available in the third year. Appendix B3 can be used to
make the calculation.

p

Appendices A5 and A6 list crop nitrogen and phosphorus requirements for various crops. These values, or crop use requirements from
other credible sources, may be used to determine the crop nitrogen needs and phosphorus removal rates for the crops included in the
crop schedule for the fields. For non-legume crops such as corn or grasses, the crop N need value represents the amount of nitrogen
required to produce the optimum yield for that crop, and is determined by multiplying the crop nitrogen requirement (in lb/bu or lb/ton
of yield) times the optimum crop yield. For legume crops such as soybeans or alfalfa, the crop utilization value represents the amount
of nitrogen these legumes will utilize from the soil in producing the optimum crop yield, provided nitrogen is available at these levels in
the soil. Again, this amount is determined by multiplying the crop utilization rate (in lb/bu or lb/ton of yield) times the optimum crop
yield.
q

As a minimum, Table 4 should indicate the full crop rotation for the management ID (i.e. , for a corn, corn, soybean rotation, Table 4
should cover a minimum of three crop years).

r

P2O5 removed with crop by harvest = P2O5 crop usage rate (Table 3) x Optimum crop yield (row 2)

s

Crop N utilization = N crop usage rate (Table 3) x Optimum crop yield (row 2)

t

Credit for nitrogen carryover from prior year legume crops should be determined as follows:
• last year’s soybean crop: 1 lb nitrogen per bushel of yield, maximum of 50 lb nitrogen per acre credit
• legume forage crop:
◊ last year’s crop with 50 to 100% alfalfa or other legume in stand: 100 to 140 lb nitrogen per acre
◊ last year’s crop with 20 to 50% alfalfa or other legume in legume/grass mixture: 50 to 80 lb nitrogen per acre
◊ two years ago crop with 50 to 100% alfalfa or other legume in stand: 30 lb nitrogen per acre
• last year’s legume green manure crop: 100 lb nitrogen per acre

u

Amount of N applied with commercial fertilizer (e.g. starter, with herbicide carrier, etc...).

v

Manure N carryover credit represents the amount of nitrogen available for crop use due to manure applications made in prior crop
years. The carryover N credit is determined by:
1. multiplying the amount of manure (in 1000 gal/acre or ton/acre) applied to the field in the previous crop by the 2nd Year
Available N concentration for the applicable manure storage source and method of application;
2. multiplying the amount of manure (in 1000 gal/acre or ton/acre) applied to the field two crop years ago by the 3nd Year
Available N concentration for the applicable manure storage source and method of application; adding the resulting N
carryover credit values together.

w

Remaining crop N need = Crop N utilization (row 4) minus (–) Legume N credit (row 5a) – Commercial N planned (row 5b) –
Manure N carryover credit (row 5c)
x

Manure rate to supply remaining N = Remaining crop N need (row 6) divided by (/) 1st year available N (Table 2) (x 1000 for liquid
manure)

y

P2O5 applied with N-based rate = Manure rate to supply remaining N need (row 7) x P2O5 concentration (Table 2) (Divide by 1000 for
liquid manure)
z

Amount of P2O5 applied with commercial fertilizers.

8

Manure Management Plan Footnotes

aa

O-53

Page 6

Manure rate to supply P removal = (P2O5 removed with crop by harvest (row 3) – Commercial P2O5 planned (row 9))/ Manure P2O5
content (Table 2) (x 1000 for liquid manure).
bb

Manure rates for a P based plan can apply up to the amount of P2O5 removed with harvest by the next 4 anticipated crops in a single
application if the application rate doesn’t exceed the N-based rate (row 7) and no additional P is applied for the period covered by the
application. For example, in a corn/soybean rotation if the “manure rate to supply P removal” (row 10) was 2,000 gal/acre for the corn
crop and 1,500 for the bean crop, then 3,500 gal/acre could be applied in a single application if the nitrogen rate was not exceeded.
Phosphorus in addition to crop removal may be applied if soil tests are very low or low in phosphorus and additional phosphorus is
recommended by Pm-1688 “General Guide to Crop Nutrient and Limestone Recommendations in Iowa.”

cc

Manure N applied with P-based plan = Manure rate for P based plan (row 11) x 1st year available N (Table 2) (divided by 1000 for
liquid manure)
dd

Manure application rate that is planned. Use these values for page 3 of the form.

ee

Field designation may be by Farm Services Agency (FSA) field number, landowner’s name, or other suitable designation. A plat map
showing the animal feeding operation and all application fields should be kept in the plan. In addition, aerial photos (e.g. FSA section
photos) of the fields receiving manure should be in the plan with the boundaries of the individual application fields marked. Also
marked on aerial photos should be areas of the fields that are unavailable or unsuitable for manure application, and areas where specific
restrictions on manure application apply. DNR may require submittal of plat maps and aerial photos. Areas with specific restrictions on
manure application include:
•

within 200 feet of a designated area: A designated area means a known sinkhole, or a cistern, abandoned well,
unplugged agricultural drainage well, agricultural drainage well surface tile inlet, drinking water well, lake, or a farm
pond or a privately owned lake as defined in Iowa Code Section 462A.2. A designated area does not include a terrace
tile inlet or surface tile inlet other than an agricultural drainage well surface tile inlet. Iowa law requires manure from an
animal feeding operation be injected or incorporated within the same day of application if applied within 200 feet of a
designated area. However, this restriction does not apply if a 50-foot buffer of permanent vegetation surrounds the
designated area and no manure is applied within the 50-foot buffer.

•

within 750 feet of neighboring residence, church, school, business, or public use area: Iowa law requires liquid manure
from a confinement feeding operation be injected or incorporated within 24 hours of application if applied within 750
feet of a neighboring residence not owned by the owner of the confinement feeding operation, a church, school, business,
or public use area. However, this restriction does not apply if a written waiver is obtained from the owner of the
property benefiting by this distance requirement.
areas where liquid manure is applied through spray irrigation systems: see footnote “t” for page 2.

•
ff

Identify how the field will be managed using management IDs from page 2.

gg

The number of acres of the field that will receive manure. Acres not available for manure application include areas where
topography, soils, or other factors make manure application impossible; areas where manure will not be applied; areas where application
is prohibited under a manure disposal agreement; and areas where Iowa law or DNR rules prohibit manure application. It may also
include areas where Iowa law or DNR rules restrict manure application to methods different than those being used by the operation.

hh

A copy of all written manure application agreements for all fields identified in the plan that are not owned or rented for crop
production purposes by the owner of the animal feeding operation must be kept with the plan (agreements must be signed by the
landowner). DNR requires submittal of manure application agreements. If manure is applied based on an agreement, also indicate in
column 6 the length of the agreement (e.g. annual, 3-yr, 10-yr).

ii

The MMP must be based on the P index in accordance with DNR rules as indicated in the table below. If the P index is required,
submit a NRCS P index detailed report containing a P index for each field in the MMP. Additionally, when the P index is required, the
manure management plan must include a document (e.g. NRCS RUSLE2 profile erosion calculation record) indicating the inputs and
results of RUSLE2 for each field in the plan (These documents must be submitted to the DNR).
Implementation Date for P-index Based Plans
Original MMP Submitted
P-index Based MMP Update Due
Prior to April 1, 2002
First update after August 25, 2008
Between April 1, 2002 and October 24, 2004
First update after August 25, 2006
On and after October 25, 2004
Upon submittal
jj

Identify if the field receiving manure is classified as Highly Erodible Land (HEL). Conservation plans are not required in the MMP
for HEL if the plan is using the P Index.
kk

gallons or tons / field = Acres receiving manure (column 5) x gallons or tons/acre (column 9)

ll

Check “yes” if soil sampling meets minimum requirements. Refer to Rule 65.17(16) in the Iowa Administrative Code for minimum
soil sampling requirements. This rule can be found in Appendix A of the MMP. If correct sampling was not used, fields must be
resampled within one year.
9

O-54

Appendix A to the

Manure Management Plan Form
Contents
Appendix A: Manure Production Per Space of Capacity .............................. 2
Appendix A2: Annual Pounds of Nitrogen Per Space of Capacity .................. 3
Appendix A3: Annual Pounds of Phosphorus (as P2O5 ) per Space of Capacity
................................................................................................ 4
Appendix A4: Nutrients in Animal Manure ...................................................... 5
Appendix A5: Crop Nitrogen Usage Rate Factors for Various Crops ............... 6
Appendix A6: Nutrient Removal for Iowa Crops .............................................. 7
Appendix A7: Nitrogen Application Losses ..................................................... 7
Appendix A8: Iowa Ag Statistics -- County Corn and Soybean Yield Averages,
200 - 2005 ............................................................................ 8
Appendix A9: Chapter 567-- 65. 6 and 567-- 65.7 Rules for Animal Feeding
Operations............................................................................. 

Revised 3/2007

542-4000


10

O-55

Appendix A
Appendix A: Manure Production Per Space of Capacity 
Daily
Swine
Nursery, 25 lb.
Grow-finish, 50 lb.
Formed storage*
Dry feed
Wet/dry feed
Earthen storage**
Lagoon***
Gestation, 400 lb.
Sow & Litter, 450 lb.
Farrow-nursery
Farrow-finish

Space
 head
 head
 head
 head
 head
 head
 crate
Per sow in
breeding herd
Per sow in
breeding herd

Yearly

Liquid, Pit*
or Basin**
0.2 gal

Liquid,
Lagoon***
0.7 gal

Solid
Manure
0.34 tons

4. gal
3.7 gal
7.5 gal
5.4 gal

2.05 tons
2.05 tons
2.05 tons
2.05 tons
2.77 tons
6.6 tons
6.09 tons

.2 gal
0.9 gal
.2 gal
3.0 gal
3.5 gal
2.2 gal
9.4 gal

30 gal

2.25 tons

Dairy, Confined
Cows, 200 & up lb.
Heifers, 900 lb.
Calves, 500 lb.
Veal calves, 250 lb.
Dairy herd

Liquid, Pit*
Space
or Basin**
 head
8.0 gal
 head
8.8 gal
 head
4.9 gal
 head
2.5 gal
Per productive 8.5 gal
cow in herd

Liquid,
Lagoon***
40. gal
29.9 gal
6.5 gal
8.2 gal
59.8 gal

Solid
Manure
4 tons
6.5 tons
.5 tons
. tons
20 tons

Beef, Confined
Mature cows, 000 lb.
Finishing, 900 lb.
Feeder calves, 500 lb.

Space
 head
 head
 head

Liquid, Pit*
or Basin**
7.2 gal
6.5 gal
3.6 gal

Liquid,
Lagoon***
5.7 gal
3. gal
7.3 gal

Solid
Manure
2.23 tons
.00 tons
6. tons

Poultry
Layer, cages
Broiler, litter
Turkeys, litter

Space
000 head
000 head
000 head

Dry Manure
0.5 tons
9.00 tons
35.00 tons

* Formed manure storage structure
** Earthen manure storage basin
*** Anaerobic lagoon



This table is from Table 5 of Chapter 567-65, Rules for Animal Feeding Operations.
542-4000 rev 7-2004

2
11

O-56
Appendix A2: Annual Pounds of Nitrogen Per Space of Capacity 2
Liquid, Pit*
or Basin**
2

Swine
Space
Nursery, 25 lb.
 head
Grow-finish, 50 lb.
Formed storage*
Dry feeders
 head
Wet/dry feeders
 head
Earthen storage**
 head
Lagoon***
 head
Gestation, 400 lb.
 head
Sow & Litter, 450 lb.
 crate
Farrow-nursery
Per sow in breeding herd
Farrow-finish
Per sow in breeding herd

Dairy, Confined
Cows, 200 & up lb.
Heifers, 900 lb.
Calves, 500 lb.
Veal calves, 250 lb.
Dairy herd

Space
 head
 head
 head
 head
Per productive
cow in herd

Beef, Confined
Mature cows, 000 lb.
Finishing, 900 lb.
Feeder calves, 500 lb.

Space
 head
 head
 head

Poultry
Layer, cages
Broiler, litter
Turkeys, litter

Space
000 head
000 head
000 head

*
**
***

2

Liquid,
Lagoon***


Solid
Manure
5

2
9
4
27
32
22
50

29
29
29
29
39
86
85
72

6
5

8
44

Liquid, Pit*
or Basin**
64
8
45
22
69

Liquid
Lagoon***
59
44
24
2
87

Solid
Manure
40
65
5
0
80

Liquid, Pit*
or Basin**
05
95
53

Liquid,
Lagoon***
23
9


Solid,
Manure
47
32
73
Dry Manure
367
585
400

Formed manure storage structure
Earthen manure storage basin
Anaerobic lagoon

This table is from Table 3 of Chapter 567-65, Rules for Animal Feeding Operations.
Source: PM 8, Managing Manure Nutrients for Crop Production
542-4000 rev 7-2004

12

3

O-57
Appendix A3:

Swine

Annual Pounds of Phosphorus (as P2O5)
per Space of Capacity3

Space

Liquid, Pit*
or Basin**

Liquid,
Lagoon***

Nursery, 25 lb.
 head

Grow-finish, 50 lb.
Formed storage*
Dry feeders
 head
5
Wet/dry feeders
 head
3
Earthen storage**
 head
0
Lagoon***
 head
Gestation, 400 lb.
 head
27
Sow & Litter, 450 lb.
 crate
26
Farrow-nursery Per sow in breeding herd 8
Farrow-finish
Per sow in breeding herd 09

Dairy, Confined

Space

Solid
Manure

0.7

3

8
8
8
8
25
55
55
0

5
4
8
6
33

Liquid, Pit*

Liquid,

or Basin**

Lagoon*** Manure

Cows, 200 & up lb
 head
Heifers, 900 lb.
 head
Calves, 500 lb.
 head
Veal calves, 250 lb.
 head
Dairy herd-per productive cow in herd

78
38
22
0
80

Beef, Confined

Space

Mature cows, 000 lb.
Finishing, 900 lb.
Feeder calves, 500 lb.

 head
 head
 head

Liquid, Pit*
or Basin**
66
59
33

Poultry
Layer, cages
Broiler, litter
Turkeys, litter

Space
000 head
000 head
000 head

Solid

44
33
8
9
66

42
20
5
3
80

Liquid,
Lagoon***
7
4
8

Solid
Manure
73
66
37

Dry Manure
840
585
400

* Formed manure storage structure
** Earthen manure storage basin
*** Anaerobic lagoon

3.

Source: Pm-8 Managing Manure Nutrients for Crop Production

4

542-4000 new 7-2004

13

O-58
Appendix A4: Nutrients in Animal Manure

(modified from Table 2 of ISU Extension Pm-8)

Management
System
Liquid, Pit

Swine
Nursery, 25 lbs.
Grow-finish, 50 lbs (wet/dry)
Grow-finish, 50 lbs. (dry feed)
Grow-finish, 50 lbs. (earthen)
Gestation, 400 lbs.
Sow and litter , 450 lbs.
Farrow-nursery 2
Farrow-finish3

N

lbs./,000 gallon Solid Manure (Bedded)
35
58
50
32
25
25
27
44

20
40
42
22
25
20
23
32

20
45
30
20
25
5
22
24

Dairy—confined
Cows, ,200 lbs. or more
Heifers, 900 lbs.
Calves, 500 lbs.
Veal calves, 250 lbs.
Dairy herd4

25
25
25
25
25

2
2
2
2
2







Beef—confined
Mature cows, ,000 lbs.
Finishing, 900 lbs.
Feeder calves, 500 lbs.

40
40
40

25
25
25

35
35
35

4

3

4

Lagoon 5

(all animals)

Management
System

P2O5 K2O

Swine—confined
Nursery, 25 lbs.
Grow-finish, 50 lbs.
Gestation, 400 lbs
Sow and litter, 450 lbs.
Farrow-nursery
Farrow-finish

N

P2O5 K2O

lbs./ton
4
4
4
4
4
4

9
9
9
9
9
9








2
2
2
2
2

6
6
6
6
6

2
2
2
2
2

Beef—confined
Mature cows, ,000 lbs. 2
Finishing, 900 lbs.
2
Feeder calves, 500 lbs. 2

6
6
6

2
2
2

Poultry
Layer, caged, 4 lbs. 6
Broiler, litter, 2 lbs.
Turkeys, litter, 0 lbs.

80
65
40

50
45
25

Dairy—confined
Cows, ,200 lbs. or more
Heifers, 900 lbs.
Calves, 500 lbs.
Veal calves, 250 lbs.
Dairy herd

35
65
40

Open Lot Runoff
Earthen lots (liquids)
Beef, 400 sq. ft./hd.
Dairy, ,000 sq. ft./hd.
Swine, 50 sq. ft./hd.

3
3
3





6
6
6

Concrete lots (liquids)
Beef, 400 sq. ft./hd.
Dairy, ,000 sq. ft./hd.
Swine, 50 sq. ft./hd.

6
6
5

2
2
5

7
7
0


2

3

4
5
6

Open lot (solids, scraped)
Beef, 400 sq. ft./hd.
22
Dairy, ,000 sq. ft./hd.

Swine, 50 sq. ft./hd.
5

6
6
4

4

9

Sow and litter figures are per farrowing crate.
Farrow-nursery figures are per sow in the breeding herd and include one farrowing sow, five gestation sows, and nine nursery pig spaces.
Farrow-finish figures are per sow in the breeding herd and include one farrowing sow, five gestation sows, nine nursery pigs,
and 36 finishing pig spaces.
Per productive cow in the herd; includes lactating cow, 330 days; dry cow, 35 days; heifer, 222 days; and calf, 65 days.
Weights assumed: beef, ,000 pounds; dairy, ,200 pounds; swine, 50 pounds.
Wet basis at 4 percent moisture.
542-4000 rev 7-2004

14

5

O-59
Appendix A5: Crop Nitrogen Usage Rate Factors for Various Crops 3
Corn

Zone 
Zone 2
Zone 3

Corn silage
Soybean
Oats
Alfalfa
Wheat
Smooth bromegrass
Sorghum-sudan

0.9 lbs/bu
. lbs/bu
.2 lbs/bu
7.5 lbs/ton
3.8 lbs/bu
0.75 lbs/bu
50.0 lbs/ton
.3 lbs/bu
40.0 lbs/ton

Orchardgrass
Tall fescue
Switchgrass
Vetch
Red clover
Perennial ryegrass
Timothy
Wheat straw
Oat straw
40.0 lbs/ton

38.0 lbs/ton
38.0 lbs/ton
2.0 lbs/ton
56.0 lbs/ton
43.0 lbs/ton
24.0 lbs/ton
25.0 lbs/ton
3.0 lbs/ton
2.0 lbs/ton

The following map outlines the three zones for the corn nitrogen usage rates indicated in the Table
4. Zone 1 corresponds to the Moody soil association. Zone 2 corresponds to the Marshall, MononaIda-Hamburg, and Galva-Primghar-Sac soil associations. Zone 3 corresponds to the remaining soil
associations.

3

3

Appendix A5 and the accompanying map are from Table 4 in Appendix B of Chapter 567-65.

542-4000 rev 7-2004

6
15

O-60
Appendix A6: Nutrient Removal for Iowa Crops4
Pounds/Unit
P2O5

K2O

Crop

Units

Corn

bu.

-

0.375

0.3

Corn Silage

ton (65% H2O)

-

3.5

8.0

Corn Silage

bu. grain equivalent

-

0.55

.25
.5

Soybean

bu.

3.8

0.8

Alfalfa

ton

50

2.5

Oat and Straw

bu.

0.75

0.4

.0

Wheat

bu.

.3

0.6

0.3

Smooth bromegrass

ton

40

9

47

Orchardgrass

ton

38

4

68

Tall fescue

ton

38

2

66

Switchgrass

ton

2

2

66

Sorghum-sudan

ton

40

2

38

Vetch

ton

56

2

47

Red clover

ton

43

2

35

Perennial ryegrass

ton

24

2

34

Timothy

ton

25

9

32

Wheat straw

ton

3

4

25

Oat straw

ton

2

5

33

40

Appendix A7: Nitrogen Application Losses
Application Loss
Factor 5

Application Method
Knifed in or soil injection of liquid manure

0.98

Surface apply liquid or solid (dry) manure with incorporation within 24 hours 0.95
Surface apply liquid or solid (dry) manure with incorporation after 24 hours 0.80
Surface apply liquid manure with no incorporation

0.75

Surface apply solid (dry) manure with no incorporation

0.70

Irrigate liquid manure with no incorporation

0.60

4. Appendix A6 is from PM 688: General Guide for Crop Nutrient Recommendations in Iowa
5. Percent of applied nitrogen remaining after deducting application losses
542-4000 rev 7-2004

7
16

O-61
Appendix A8: Iowa Ag Statistics
County Corn and Soybean Yield Averages, 2004 - 2008
Corn
County

5-yr. avg.
yield
(bu./a)

5-yr. ave.
yield + 0%
(bu./a)

Soybeans
Avg. yield
of 4 highest
(bu./a)

5-yr. avg.
yield
(bu./a)

5-yr. ave.
yield + 0%
(bu./a)

Avg. yield
of 4 highest
(bu./a)

Adair

67.

83.9

69.2

50.0

55.0

5.2

Adams

56.2

7.9

59.0

47.2

5.9

49.4

Allamakee

68.8

85.7

70.2

47.6

52.4

49.2

Appanoose

49.9

64.9

57.9

43.0

47.3

46.

Audubon

73.5

90.8

76.7

52.

57.3

52.8

Benton

74.5

9.9

75.6

52.3

57.5

52.8

Black Hawk

77.2

94.9

80.3

52.

57.4

52.8

Boone

8.

99.2

84.9

5.2

56.3

53.

Bremer

80.6

98.7

85.5

5.8

57.0

53.7

Buchanan

72.7

89.9

75.

49.6

54.6

50.7

Buena Vista

72.6

89.9

80.0

50.3

55.3

50.9

Butler

80.3

98.3

8.6

5.0

56.

52.0

Calhoun

78.

95.9

8.2

49.6

54.6

50.5

Carroll

76.3

93.9

79.7

50.6

55.6

5.0

Cass

72.6

89.8

76.3

50.6

55.6

5.9

Cedar

75.8

93.4

83.7

49.8

54.8

50.3

Cerro Gordo

72.

89.3

73.6

48.2

53.0

49.2

Cherokee

75.9

93.5

83.8

55.

60.6

55.4

Chickasaw

72.9

90.2

76.4

49.4

54.3

50.6

Clarke

42.

56.4

50.4

4.5

45.6

45.3

Clay

72.9

90.2

76.3

48.9

53.8

49.3

Clayton

75.0

92.5

76.0

52.7

58.0

53.6

Clinton

65.5

82.0

77.7

48.5

53.3

50.0

Crawford

70.0

87.0

77.8

5.6

56.8

52.3

Dallas

74.8

92.3

77.5

52.2

57.4

53.6

Davis

5.2

66.4

60.3

44.5

48.9

46.6

Decatur

52.9

68.2

63.

45.4

49.9

49.0

Delaware

74.6

92.

78.5

52.

57.3

53.6

Des Moines

77.6

95.4

83.4

50.6

55.7

5.6

Dickinson

70.4

87.4

73.3

47.2

52.0

48.2

Dubuque

77.7

95.5

82.7

52.7

58.0

54.9

Emmet

74.8

92.3

77.

48.2

53.0

49.2

Fayette

73.7

9.

75.5

50.8

55.9

52.4
updated 3/2009

8
17

O-62
Appendix A8: Iowa Ag Statistics
County Corn and Soybean Yield Averages, 2004 - 2008

Counties

5-yr. avg.
yield
(bu./a)

Corn

5-yr. ave.
yield + 0%
(bu./a)

Soybeans
Avg. yield
of 4 highest
(bu./a)

5-yr. avg.
yield
(bu./a)

5-yr. ave.
yield + 0%
(bu./a)

Avg. yield
of 4 highest
(bu./a)

Floyd

73.5

90.9

75.7

49.0

53.9

50.2

Franklin

79.4

97.3

82.5

49.3

54.3

50.6

Fremont

58.7

74.6

6.9

48.0

52.8

49.8

Greene

76.3

93.9

80.6

49.9

54.9

50.9

Grundy

82.9

20.

84.6

56.0

6.6

56.8

Guthrie

64.6

8.

66.

47.7

52.5

48.8

Hamilton

78.5

96.4

83.9

49.7

54.6

50.5

Hancock

76.9

94.5

78.3

50.0

55.0

5.6

Hardin

80.5

98.5

85.9

52.8

58.0

54.0

Harrison

62.4

78.7

67.5

44.4

48.8

45.6

Henry

72.5

89.8

77.4

50.7

55.7

5.5

Howard

68.7

85.6

70.7

47.

5.8

48.8

Humboldt

8.8

200.0

84.3

50.5

55.6

5.3

Ida

70.6

87.6

8.9

49.8

54.7

50.6

Iowa

72.4

89.7

78.7

50.9

56.0

52.0

Jackson

59.7

75.7

68.6

49.2

54.

50.0

Jasper

83.9

202.3

86.4

54.9

60.4

55.5

Jefferson

62.9

79.

67.7

48.

53.0

49.8

Johnson

62.7

79.0

69.4

47.7

52.4

48.2

Jones

68.

84.9

73.0

49.9

54.9

50.9

Keokuk

64.7

8.2

72.2

49.3

54.3

50.2

Kossuth

78.5

96.4

80.4

50.2

55.2

52.0

Lee

60.8

76.9

68.7

47.2

5.9

48.5

Linn

69.9

86.8

74.3

48.8

53.7

49.4

Louisa

66.9

83.6

75.3

47.4

52.2

47.9

Lucas

40.7

54.7

47.3

42.

46.3

45.6

Lyon

77.7

95.5

8.3

53.2

58.5

54.0

Madison

63.3

79.6

65.4

48.9

53.8

50.8

Mahaska

75.0

92.5

78.7

52.2

57.5

53.6

Marion

59.

75.0

63.

49.0

53.9

50.

Marshall

85.4

204.0

86.8

55.7

6.3

57.0

Mills

62.3

78.5

66.0

48.5

53.4

50.4

Mitchell

76.

93.7

77.5

49.6

54.5

5.0
9

18

O-63
Appendix A8: Iowa Ag Statistics
County Corn and Soybean Yield Averages, 2004 - 2008
Corn

5-yr. ave.
yield + 0%
(bu./a)

Soybeans

Counties

5-yr. avg.
yield
(bu./a)

Avg. yield
of 4 highest
(bu./a)

Monona

5.3

66.4

6.8

44.8

49.3

45.4

Monroe

52.0

67.2

56.0

43.9

48.3

46.7

Montgomery

62.

78.3

66.3

48.0

52.8

50.6

Muscatine

65.7

82.2

73.3

48.0

52.8

49.

O Brien

79.2

97.

82.5

54.2

59.6

55.6

Osceola

77.0

94.7

79.9

5.2

56.4

52.2

Page

53.9

69.3

59.2

47.6

52.3

50.2

Palo Alto

75.8

93.4

79.

49.2

54.2

50.5

Plymouth

67.3

84.0

74.8

50.

55.

50.4

Pocahontas

78.

95.9

8.0

49.8

54.8

50.8

Polk

72.4

89.6

77.0

49.4

54.3

50.8

Pottawattamie

74.6

92.0

77.6

50.5

55.5

52.9

Poweshiek

79.5

97.5

8.9

53.8

59.2

55.2

Ringgold

40.9

55.0

47.4

42.9

47.2

47.2

Sac

72.4

89.6

82.0

50.9

56.0

5.9

Scott

75.5

93.

82.2

52.2

57.4

52.6

Shelby

75.5

93.0

77.5

5.3

56.4

52.

Sioux

77.5

95.3

82.7

55.2

60.7

55.6

Story

80.

98.

85.

52.0

57.2

53.5

Tama

78.9

96.8

80.4

53.9

59.3

55.

Taylor

45.9

60.5

48.7

44.6

49.0

47.3

Union

54.7

70.

56.3

47.0

5.7

49.4

Van Buren

53.8

69.2

6.3

46.5

5.

48.0

Wapello

57.9

73.7

63.3

47.5

52.3

48.9

Warren

56.4

72.0

6.8

49.7

54.7

5.9

Washington

74.7

92.

80.

50.5

55.6

50.9

Wayne

42.4

56.6

52.3

44.6

49.0

48.2

Webster

8.

99.2

84.6

49.3

54.2

49.9

Winnebago

8.

99.2

82.9

49.9

54.9

5.9

Winneshiek

74.6

92.

75.8

48.7

53.6

50.

Woodbury

6.3

77.4

69.2

45.9

50.5

46.4

Worth

75.3

92.8

76.6

47.8

52.6

49.6

Wright

79.5

97.4

83.4

50.0

55.0

5.0

0
19

5-yr. avg.
yield
(bu./a)

5-yr. ave.
yield + 0%
(bu./a)

Avg. yield
of 4 highest
(bu./a)

O-64
Appendix A9: Chapter 567-- 65. 6 and 567-- 65.7 Rules for Animal Feeding
Operations
Please note: Manure management plans that include the phosphorus index will be phased in between the fall of 2004 and 2008, depending upon the date that the original MMP was submitted to
the DNR. See 65.17(1)”d” below for the phase in schedule.
Disclaimer: Producers should consult Chapter 65 of the Iowa Administrative Code for more information and the actual wording of rules governing animal feeding operations. Consult Chapter 459 of
the Iowa Code for actual wording of the laws governing animal feeding operations in Iowa.

567—65.6(455B) Manure management plan requirements.
65.16(1) In accordance with Iowa Code section 455B.203 as amended by 2002 Iowa Acts, chapter 1137, section 38, the following persons are required to submit manure management plans to the department, including
an original manure management plan and an updated manure management plan, as required by this rule:
a. An applicant for a construction permit for a confinement feeding operation. However, a manure management plan shall not be required of an applicant for an egg washwater storage structure.
b. The owner of a confinement feeding operation, other than a small animal feeding operation, if one of the
following applies:
(1) The confinement feeding operation was constructed or expanded after May 31, 1985, regardless of whether the confinement feeding operation structure was required to have a construction permit.
(2) The owner constructs a manure storage structure, regardless of whether the person is required to be issued
a permit for the construction pursuant to Iowa Code section 455B.200A as amended by 2002 Iowa Acts, chapter 1137, sections 28 and 29, or whether the person has submitted a prior manure management plan.
c. A person who applies manure in Iowa that was produced in a confinement feeding operation, other than a
small operation, located outside of Iowa.
d. A research college is exempt from this subrule and the manure management plan requirements of rule
65.17(459) for research activities and experiments performed under the authority of the research college and
related to animal feeding operations.
65.16(2) Effective February 13, 2002, an owner of a proposed confinement feeding operation who is required
to file a manure management plan pursuant to paragraph 65.16(1)“b” shall submit the confinement
feeding operation’s manure management plan to the department at least 30 days before the construction of
an animal feeding operation structure begins, as that term is defined in subrules 65.8(1) and 65.8(2). After
the manure management plan has been received by the department, the department will date-stamp the plan
as received and provide written confirmation of receipt to the owner. In addition to the content requirements
specified in rule 65.17(459), the owner shall include:
a. Documentation that the board of supervisors or auditor of the county where the confinement feeding operation is proposed to be located received a copy of the plan.
b. Information (e.g., maps, drawings, aerial photos) that clearly shows the intended location of the animal
feeding operation structures and locations and animal weight capacities of any other confinement feeding
operations within a distance of 2,500 feet in which the owner has an ownership interest or which the owner
manages.
65.16(3) Scope of manure management plan; updated plans; annual compliance fee.
a. Each confinement feeding operation required to submit a manure management plan shall be covered by a
separate manure management plan.
updated 8/2005

20



O-65
b. The owner of a confinement feeding operation who is required to submit a manure management plan under
this rule shall submit an updated manure management plan on an annual basis to the department. The updated
plan must reflect all amendments made during the period of time since the previous manure management plan
submission. The owner of the animal feeding operation shall also submit the updated manure management
plan on an annual basis to the board of supervisors of each county where the confinement feeding operation is
located and to the board of supervisors of each county where manure from the confinement feeding operation
is land-applied. If the owner of the animal feeding operation has not previously submitted a manure management plan to the board of supervisors of each county where the confinement feeding operation is located and
each county where manure is land-applied, the owner must submit a complete manure management plan to
each required county. The county auditor or other county official or employee designated by the county board
of supervisors may accept the updated plan on behalf of the board. The updated plan shall include documentation that the county board of supervisors or other designated county official or employee received the manure
management plan update. The department will stagger the dates by which the updated manure management
plans are due and will notify each confinement feeding operation owner of the date on which the updated manure management plan is due. To satisfy the requirements of an updated manure management plan, an owner
of a confinement feeding operation must submit one of the following:
(1) A complete manure management plan;
(2) A department-approved document stating that the manure management plan submitted in the prior year has
not changed; or
(3) A department-approved document listing all the changes made since the previous manure management
plan was submitted and approved.
c. An annual compliance fee of $0.15 per animal unit at the animal feeding operation shall accompany an annual manure management plan update submitted to the department for approval. The annual compliance fee
is based on the animal unit capacity of the confinement feeding operation stated in the updated annual manure
management plan submission. If the person submitting the manure management plan is a contract producer, as
provided in Iowa Code chapter 202, the active contractor shall pay the annual compliance fee.
65.16(4) The department shall review and approve or disapprove all complete manure management plans
within 60 days of the date they are received.
65.16(5) Manure shall not be removed from a manure storage structure, which is part of a confinement feeding operation required to submit a manure management plan, until the department has approved the plan.
As an exception to this requirement, until July 1, 2002, the owner of a confinement feeding operation may
remove and apply manure from a manure storage structure in accordance with a manure management plan
submitted to the department prior to September 18, 2001, but which has not been approved within the required 60-day period. Manure shall be applied in compliance with rule 65.2(455B).
\65.16(6) All persons required to submit a manure management plan to the department shall also pay to the
department an indemnity fee as required in Iowa Code section 455J.3 except those operations constructed
prior to May 31, 1995, which were not required to obtain a construction permit.
65.16(7) Any person submitting an original manure management plan must also pay to the department a manure management plan filing fee of $250. This fee shall be included with each original manure management
plan being submitted. If the confinement feeding operation is required to obtain a construction permit and to
submit an original manure management plan as part of the construction permit requirements, the applicant
must pay the manure management plan filing fee together with the construction permit application fee, which
total $500.

567—65.7(459) Manure management plan content requirements. All manure management

plans are to be submitted on forms or electronically as prescribed by the department. The plans shall include
all of the information specified in Iowa Code section 459.312 and as described below.

2
21

O-66
65.17(1) General.
a. A confinement feeding operation that is required to submit a manure management plan to the department
shall not apply manure in excess of the nitrogen use levels necessary to obtain optimum crop yields. When
a phosphorus index is required in a manure management plan as provided in 65.17(1)“d,” a confinement
feeding operation shall not apply manure in excess of the rates determined in conjunction with the phosphorus index. Information to complete the required calculations may be obtained from the tables in this chapter,
actual testing samples or from other credible sources including, but not limited to, Iowa State University, the
United States Department of Agriculture (USDA), a licensed professional engineer, or an individual certified
as a crop consultant under the American Registry of Certified Professionals in Agronomy, Crops, and Soils
(ARCPACS) program, the Certified Crop Advisors (CCA) program, or the Registry of Environmental and
Agricultural Professionals (REAP) program.
b. Manure management plans shall comply with the minimum manure control requirements of 65.2(455B)
and the requirements for land application of manure in 65.3(455B).
c. Manure management plans shall include all of the following:
(1) The name of the owner and the name of the confinement feeding operation, including mailing address and
telephone number.
(2) The name of the contact person for the confinement feeding operation, including mailing address and
telephone number.
(3) The location of the confinement feeding operation identified by county, township, section, 1/4 section and,
if available, the 911 address.
(4) The animal unit capacity of the confinement feeding operation and, if applicable, the animal weight capacity.
d. A person who submits a manure management plan shall include a phosphorus index as part of the manure
management plan as follows:
(1) A person who submitted an original manure management plan prior to April 1, 2002, shall submit a phosphorus index with the first manure management plan update on and after August 25, 2008.
(2) A person who submitted an original manure management plan on or after April 1, 2002, but prior to October 25, 2004, shall submit a phosphorus index with the first manure management plan update on and after
August 25, 2006.
(3) A person who submits an original manure management plan on and after October 25, 2004, shall include
the phosphorus index as part of the original manure management plan and manure management plan updates.
65.17(2) Manure management plans for sales of manure. Selling manure means the transfer of ownership of
the manure for monetary or other valuable consideration. Selling manure does not include a transaction where
the consideration is the value of the manure, or where an easement, lease or other agreement granting the right
to use the land only for manure application is executed.
a. Confinement feeding operations that will sell dry manure as a commercial fertilizer or soil conditioner
regulated by the Iowa department of agriculture and land stewardship (IDALS) under Iowa Code chapter 200
or 200A shall submit a copy of their site-specific IDALS license or documentation that manure will be sold
pursuant to Iowa Code chapter 200 or 200A, along with the departmentapproved manure management plan
form for sales of dry manure. Operations completely covered by this paragraph are not required to meet other
manure management plan requirements in this rule.
b. A confinement feeding operation not fully covered by paragraph “a” above and that has an established
practice of selling manure, or a confinement feeding operation that contains an animal species for which elling manure is a common practice, shall submit a manure management plan that includes the following:
(1) Until a phosphorus index is required as part of the manure management plan, an estimate of the number of
acres required for manure application shall be calculated by dividing the total nitrogen available to be applied
from the confinement feeding operation by the crop usage rate. Crop usage rate may be estimated by using a
corn crop usage rate factor and an estimate of the optimum crop yield for the property in the vicinity of the
confinement feeding operation.
(2) When a phosphorus index is required as part of the manure management plan, an estimate of the number
of acres required for manure application shall be calculated by one of the following methods:
3
22

O-67
1. Dividing the total phosphorus (as P2O5) available to be applied from the confinement feeding operation by
the corn crop removal of phosphorus. The corn crop removal of phosphorus may be estimated by using the
phosphorus removal rate in Table 4a at the end of this chapter and an estimate of the optimum crop yieldfor
the property in the vicinity of the operation.
2. Totaling the quantity of manure that can be applied to each available field based on application rates determined in conjunction with the phosphorus index in accordance with 65.17(17), and ensuring that the total
quantity that can be applied is equal to or exceeds the manure annually generated at the operation.
(3) The total nitrogen available to be applied from the confinement feeding operation.
(4) The total phosphorus (as P2O5) available to be applied from the confinement feeding operation if the
phosphorus index is required in accordance with 65.17(1)“d.”
(5) An estimate of the annual animal production and manure volume or weight produced.
(6) A manure sales form, if manure will be sold, shall include the following information:
1. A place for the name and address of the buyer of the manure.
2. A place for the quantity of manure purchased.
3. The planned crop schedule and optimum crop yields.
4. A place for the manure application methods and the timing of manure application.
5. A place for the location of the field including the number of acres where the manure will be applied.
6. A place for the manure application rate.
7. When a phosphorus index is required as part of a manure management plan in accordance with
65.17(1)“d,” a place for a phosphorus index of each field receiving manure, as defined in 65.17(17)“a,” including the factors used in the calculation. A copy of the NRCS phosphorus index detailed report shall satisfy
the requirement to include the factors used in the calculation.
(7) Statements of intent if the manure will be sold. The number of acres indicated in the statements of intent
shall be sufficient according to the manure management plan to apply the manure from the confinement feeding operation. The permit holder for an existing confinement feeding operation with a construction permit
may submit past records of manure sales instead of statements of intent. The statements of intent shall include
the following information:
1. The name and address of the person signing the statement.
2. A statement indicating the intent of the person to purchase the confinement feeding operation’s manure.
3. The location of the farm where the manure can be applied including the total number of acres available for
manure application.
4. The signature of the person who may purchase the confinement feeding operation’s manure.
(8) The owner shall maintain in the owner’s records a current manure management plan and copies of all of
the manure sales forms; the sales forms must be completed and signed by each buyer of the manure and the
applicant, and the copies must be maintained in the owner’s records for three years after each sale. Effective
August 25, 2006, the owner shall maintain in the owner’s records copies of all of the manure sales forms for
five years after each sale. An owner of a confinement feeding operation shall not be required to maintain current statements of intent as part of the manure management plan.
65.17(3) Manure management plan for nonsales of manure. Confinement feeding operations that will not sell
all of their manure shall submit the following for that portion of the manure which will not be sold:
a. Calculations to determine the land area required for manure application.
b. The total nitrogen available to be applied from the confinement feeding operation.
c. The planned crop schedule and optimum crop yields.
d. Manure application methods and timing of the application.
e. The location of manure application.
f. An estimate of the annual animal production and manure volume or weight produced.
g. Methods, structures or practices that will be used to reduce soil loss and prevent surface water pollution.
h. Methods or practices that will be utilized to reduce odor if spray irrigation equipment is used to apply manure.
i. When a phosphorus index is required as part of the manure management plan in accordance with
65.17(1)“d,” the following are required:
4
23

(1) The total phosphorus (as P2O5) available to be applied from the confinement feeding operation.
(2) A phosphorus index of each field in the manure management plan, as defined in 65.17(17)“a,” including the factors used in the calculation. A copy of the NRCS phosphorus index detailed report shall satisfy the
requirement to include the factors used in the calculation.
65.17(4) Manure management plan calculations to determine land area required for manure application.
a. The number of acres needed for manure application for each year of the crop schedule shall be determined
as follows:
(1) Until a phosphorus index is required in accordance with 65.17(1)“d,” the requirements of 65.17(18) shall
be followed.
(2) When a phosphorus index is required in accordance with 65.17(1)“d,” the requirements of 65.17(17) shall
be followed.
b. Operations evaluated with the master matrix pursuant to 65.10(3) that claim points for additional separation
distance for the land application of manure must maintain those distances for each year of the manure management plan.
c. Nitrogen in addition to that allowed in the manure management plan may be applied up to the amounts,
indicated by soil or crop nitrogen test results, necessary to obtain the optimum crop yield.
65.17(5) Total nitrogen and total phosphorus (as P2O5) available from the confinement feeding operation.
a. To determine the nitrogen available to be applied per year, the factors in Table 3, “Annual Pounds of Nitrogen Per Space of Capacity,” multiplied by the number of spaces shall be used. To determine total phosphorus
(as P2O5) available to be applied per year, the factors in Table 3a, “Annual Pounds of Phosphorus Per Space
of Capacity,” multiplied by the number of spaces shall be used. If the tables are not used to determine the nitrogen or phosphorus available to be applied, other credible sources for standard table values or the actual nitrogen and phosphorus content of the manure may be used. The actual nitrogen and phosphorus content shall
be determined by a laboratory analysis along with measured volume or weight of manure from the manure
storage structure or from a manure storage structure with design and management similar to the confinement
feeding operation’s manure storage structure.
b. If an actual sample is used to represent the nutrient content of manure, the sample shall be taken in accordance with Iowa State University extension publication PM 1558, “Management Practices: How to Sample
Manure for Nutrient Analysis.” The department may require documentation of the manure sampling protocol
or take a split sample to verify the nutrient content of the operation’s manure.
65.17(6) Optimum crop yield and crop schedule.
a. To determine the optimum crop yield, the applicant may either exclude the lowest crop yield for the period of the crop schedule in the determination or allow for a crop yield increase of 10 percent. In using these
methods, adjustment to update yield averages to current yield levels may be made if it can be shown that the
available yield data is not representative of current yields. The optimum crop yield shall be determined using
any of the following methods for the cropland where the manure is to be applied:
(1) Soil survey interpretation record. The plan shall include a map showing soil map units for the fields where
manure will be applied. The optimum crop yield for each field shall be determined by using the weighted
average of the soil interpretation record yields for the soils on the cropland where the manure is to be applied.
Soil interpretation records from the Natural Resources Conservation Service shall be used to determine yields
based on soil map units.
(2) USDA county crop yields. The plan shall use the county yield data from the USDA Iowa Agricultural
Statistics Service.
(3) Proven yield methods. Proven yield methods may only be used if a minimum of the most recent three
years of yield data for the crop is used. These yields can be proven on a field-by-field or farm-by-farm basis.
Crop disaster years may be excluded when there is a 30 percent or more reduction in yield for a particular
field or farm from the average yield over the most recent five years. Excluded years shall be replaced by the
most recent nondisaster years. Proven yield data used to determine application rates shall be maintained with
the current manure management plan. Any of the following proven yield methods may be used:
1. Proven yields for USDA Farm Service Agency. The plan shall use proven yield data or verified yield data
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for Farm Service Agency programs.
2. Proven yields for multiperil crop insurance. Yields established for the purpose of purchasing multiperil crop
insurance shall be used as proven yield data.
3. Proven yields from other methods. The plan shall use the proven yield data and indicate the method used in
determining the proven yield.
b. Crop schedule. Crop schedules shall include the name and total acres of the planned crop on a field-by-field
or farm-by-farm basis where manure application will be made. A map may be used to indicate crop schedules
by field or farm. The planned crop schedule shall name the crop(s) planned to be grown for the length of the
crop rotation beginning with the crop planned or actually grown during the year this plan is submitted or the
first year manure will be applied. The confinement feeding operation owner shall not be penalized for exceeding the nitrogen or phosphorus application rate for an unplanned crop, if crop schedules are altered because of
weather, farm program changes, market factor changes, or other unforeseeable circumstances.
65.17(7) Manure application methods and timing.
a. The manure management plan shall identify the methods that will be used to land-apply the confinement
feeding operation’s manure. Methods to land-apply the manure may include, but are not limited to, surfaceapply dry with no incorporation, surface-apply liquids with no incorporation, surface-apply liquid or dry with
incorporation within 24 hours, surface-apply liquid or dry with incorporation after 24 hours, knifed in or soil
injection of liquids, or irrigated liquids with no incorporation.
b. The manure management plan shall identify the approximate time of year that land application of manure is
planned. The time of year may be identified by season or month.
65.17(8) Location of manure application.
a. The manure management plan shall identify each farm where the manure will be applied, the number of
acres that will be available for the application of manure from the confinement feeding operation,
and the basis under which the land is available.
b. A copy of each written agreement executed with the owner of the land where manure will be applied shall
be maintained with the current manure management plan. The written agreement shall indicate the acres on
which manure from the confinement feeding operation may be applied and the length of the agreement. A
written agreement is not required if the land is owned or rented for crop production by the owner of the confinement feeding operation.
c. If a present location becomes unavailable for manure application, additional land for manure application
shall be identified in the current manure management plan prior to the next manure application period.
65.17(9) Estimate of annual animal production and manure volume or weight produced. Volumes or weights
of manure produced shall be estimated based on the numbers of animals, species, and type of manure storage used. The plan shall list the annually expected number of production animals by species. The volume of
manure may be estimated based on the values in Table 5 at the end of this chapter and submitted as a part of
the plan. If the plan does not use the table to determine the manure volume, other credible sources for standard
table values or the actual manure volume from the confinement feeding operation may be used.
65.17(10) Methods to reduce soil loss and potential surface water pollution. The manure management plan
shall include an identification of the methods, structures or practices that will be used to prevent or diminish
soil loss and potential surface water pollution during the application of manure. Until a phosphorus index is
required in accordance with 65.17(1)“d,” the current manure management plan shall maintain a summary
or copy of the conservation plan for the cropland where manure from the animal feeding operation will be
applied if the manure will be applied on highly erodible cropland. The conservation plan shall be the conservation plan approved by the local soil and water conservation district or its equivalent. The summary of the
conservation plan shall identify the methods, structures or practices that are contained in the conservation
plan. When a phosphorus index is required in accordance with 65.17(1)“d,” the manure management plan
shall indicate for each field in the plan the crop rotation, tillage practices and supporting practices used to calculate sheet and rill erosion for the phosphorus index. A copy of the NRCS RUSLE2 profile erosion calculation record shall satisfy the requirement to indicate the crop rotation, tillage practices and supporting practices
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to calculate sheet and rill erosion. The plan shall also identify the highly erodible cropland where manure will be
applied. The manure management plan may include additional information such as whether the manure will be
injected or incorporated or the type of manure storage structure.
65.17(11) Spray irrigation. Requirements contained in subrules 65.3(2) and 65.3(3) regarding the use of spray
irrigation equipment to apply manure shall be followed. A plan which has identified spray irrigation equipment
as the method of manure application shall identify any additional methods or practices to reduce potential odor, if
any other methods or practices will be utilized.
65.17(12) Current manure management plan. The owner of a confinement feeding operation who is required to
submit a manure management plan shall maintain a current manure management plan at the site of the confinement feeding operation or at a residence or office of the owner or operator of the operation within 30 miles of
the site. The plan shall include completed manure sales forms for a confinement feeding operation from which
manure is sold. If manure management practices change, a person required to submit a manure management plan
shall make appropriate changes consistent with this rule. If values other than the standard table values are used
for manure management plan calculations, the source of the values used shall be identified.
65.17(13) Record keeping. Records shall be maintained by the owner of a confinement feeding operation who
is required to submit a manure management plan. This recorded information shall be maintained for three years
following the year of application or for the length of the crop rotation, whichever is greater. Effective August 25,
2006, records shall be maintained for five years following the year of application or for the length of the crop
rotation, whichever is greater. Records shall be maintained at the site of the confinement feeding operation or at
a residence or office of the owner or operator of the facility within 30 miles of the site. Records to demonstrate
compliance with the manure management plan shall include the following:
a. Factors used to calculate the manure application rate:
(1) Optimum yield for the planned crop.
(2) Types of nitrogen credits and amounts.
(3) Remaining crop nitrogen needed.
(4) Nitrogen content and first-year nitrogen availability of the manure.
(5) Phosphorus content of the manure if required in accordance with 65.17(3)“i.” If an actual sample is used,
documentation shall be provided.
b. If phosphorus-based application rates are used, the following shall be included:
(1) Crop rotation.
(2) Phosphorus removed by crop harvest of that crop rotation.
c. Maximum allowable manure application rate.
d. Actual manure application information:
(1) Methods of application when manure from the confinement feeding operation was applied.
(2) Date(s) when the manure from the confinement feeding operation was applied.
(3) Location of the field where the manure from the confinement feeding operation was applied, including the
number of acres.
(4) The manure application rate.
e. Effective August 25, 2005, date(s) and application rate(s) of commercial nitrogen and phosphorus on fields
that received manure. However, if the date and application rate information is for fields which are not owned for
crop production or which are not rented or leased for crop production by the person required to keep records pursuant to this subrule, an enforcement action for noncompliance with a manure management plan or the requirements of this subrule shall not be pursued against the person required to keep records pursuant to this subrule or
against any other person who relied on the date and application rate in records required to be kept pursuant to this
subrule, unless that person knew or should have known that nitrogen or phosphorus would be applied in excess
of maximum levels set forth in paragraph 65.17(1)“a.” If manure is applied to fields not owned, rented or leased
for crop production by the person required to keep records pursuant to this subrule, that person shall obtain from
the person who owns, rents or leases those fields a statement specifying the planned commercial nitrogen and
phosphorus fertilizer rates to be applied to each field receiving the manure.
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f. When a phosphorus index is required in accordance with 65.17(1)“d,” a copy of the current soil test lab
results for each field in the manure management plan.
g. For sales of manure under 65.17(2)“b,” record-keeping requirements of 65.17(2)“b”(8) shall be followed.
65.17(14) Record inspection. The department may inspect a confinement feeding operation at any time during
normal working hours and may inspect the manure management plan and any records required to be maintained. As required in Iowa Code section 459.312(12), Iowa Code chapter 22 shall not apply to the records
which shall be kept confidential by the department and its agents and employees. The contents of the records
are not subject to disclosure except as follows:
a. Upon waiver by the owner of the confinement feeding operation.
b. In an action or administrative proceeding commenced under this chapter. Any hearing related to the action
or proceeding shall be closed.
c. When required by subpoena or court order.
65.17(15) Enforcement action. An owner required to provide the department a manure management plan
pursuant to this rule who fails to provide the department a plan or who is found in violation of the terms and
conditions of the plan shall not be subject to an enforcement action other than assessment of a civil penalty
pursuant to Iowa Code section 455B.191.
65.17(16) Soil sampling requirements for fields where the phosphorus index must be used. Soil samples shall
be obtained from each field in the manure management plan at least once every four years. Each soil sample
shall be analyzed for phosphorus and pH. The soil sampling protocol shall meet all of the following requirements:
a. Acceptable soil sampling strategies include, but are not limited to, grid sampling, management zone sampling, and soil type sampling. Procedural details can be taken from Iowa State University extension publication PM 287, “Take a Good Soil Sample to Help Make Good Decisions,” NCR-13 Report 348, “Soil Sampling for Variable-Rate Fertilizer and Lime Application,” or other credible soil sampling publications.
b. Each soil sample must be a composite of at least ten soil cores from the sampling area, with each core containing soil from the top six inches of the soil profile.
c. Each soil sample shall represent no more than ten acres. For fields less than or equal to 15 acres, only one
soil sample is necessary.
d. Soil analysis must be performed by a lab enrolled in the IDALS soil testing certification program.
e. The soil phosphorus test method must be an appropriate method for use with the phosphorus index. If soil
pH is greater than or equal to 7.4, soil phosphorus data from the Bray-1 extraction method is not acceptable
for use with the phosphorus index.IA
C 7/21/04
65.17(17) Use of the phosphorus index. Manure application rates shall be determined in conjunction with the
use of the Iowa Phosphorus Index as specified by the USDA Natural Resources Conservation Service (NRCS)
Iowa Technical Note No. 25.
a. The phosphorus index shall be used on each individual field in the manure management plan. The fields
must be contiguous and shall not be divided by a public thoroughfare or a water source as each is defined in
this chapter. Factors to be considered when a field is defined may include, but are not limited to, cropping system, erosion rate, soil phosphorus concentration, nutrient application history, and the presence of site-specific
soil conservation practices.
b. When sheet and rill erosion is calculated for the phosphorus index, the soil type used for the calculation
shall be the most erosive soil map unit that is at least 10 percent of the total field area.
c. The average (arithmetic mean) soil phosphorus concentration of a field shall be used in the phosphorus
index.
d. Soil phosphorus concentration data is considered valid for use in the phosphorus index if the data is four
years old or less and meets the requirements of 65.17(16).
e. For an original manure management plan, previous soil sampling data that does not meet the requirements
of 65.17(16) may be used in the phosphorus index if the data is four years old or less. In the case of fields for
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which soil sampling data is used that does not meet the requirements of 65.17(16), the fields must be soilsampled according to the requirements of 65.17(16) no more than one year after the manure management plan
is approved.
f. The following are the manure application rate requirements for fields that are assigned the phosphorus index
site vulnerability ratings below as determined by the NRCS Iowa Technical Note No. 25 to the NRCS 590
standard rounded to the nearest one-hundredth:
(1) Very Low (0-1).
1. Manure shall not be applied in excess of a nitrogen-based rate in accordance with 65.17(18).
2. If, pursuant to 65.17(19), manure is applied at phosphorus-based rates within soil sampling periods on
fields in the Very Low risk category, each soil sample may represent up to 20 acres for the next required soil
sampling.
(2) Low (>1-2).
1. Manure shall not be applied in excess of a nitrogen-based rate in accordance with 65.17(18).
2. If, pursuant to 65.17(19), manure is applied at phosphorus-based rates within soil sampling periods on
fields in the Low risk category, each soil sample may represent up to 20 acres for the next required soil sampling.
(3) Medium (>2-5).
1. Manure may be applied at a nitrogen-based rate in accordance with 65.17(18) if current or planned soil
conservation and phosphorus management practices predict the rating of the field to be not greater than 5 for
the next determination of the phosphorus index as required by 65.17(17)“h”(3).
2. Manure shall not be applied in excess of two times the phosphorus removed with crop harvest over the
period of the crop rotation.
3. If, pursuant to 65.17(19), manure is applied at phosphorus-based rates within soil sampling periods on
fields in the Medium risk category, each soil sample may represent up to 20 acres for the next required soil
sampling.
(4) High (>5-15). Manure shall not be applied on a field with a rating greater than 5 and less than or equal to
15 until practices are adopted which reduce the phosphorus index to at least the Medium risk category. However, prior to December 31, 2008, fields with a phosphorus index greater than 5 and less than or equal to 10
may receive manure at a phosphorus-based rate in accordance with 65.17(19) if practices will be adopted to
reduce the phosphorus index to the Medium risk category.
(5) Very High (>15). Manure shall not be applied on a field with a rating greater than 15.
g. Additional commercial fertilizer may be applied as follows on fields receiving manure:
(1) Phosphorus fertilizer may be applied in addition to phosphorus provided by the manure up to amounts recommended by soil tests and Iowa State University extension publication PM 1688, “General Guide for Crop
Nutrient Recommendations in Iowa.”
(2) Nitrogen fertilizer may be applied in addition to nitrogen provided by the manure to meet the remaining
nitrogen need of the crop as calculated in the current manure management plan. Additional nitrogen fertilizer
may be applied up to the amounts indicated by soil test nitrogen results or crop nitrogen test results as necessary to obtain the optimum crop yield.
h. Updating the phosphorus index.
(1) When any inputs to the phosphorus index change, an operation shall recalculate the phosphorus index and
adjust the application rates if necessary.
(2) If additional land becomes available for manure application, the phosphorus index shall be calculated to
determine the manure application rate before manure is applied.
(3) An operation must submit a complete manure management plan using a new phosphorus index for each
field in the manure management plan a minimum of once every four years.
65.17(18) Requirements for application of a nitrogen-based manure rate to a field.
a. Nitrogen-based application rates shall be based on the total nitrogen content of the manure unless the calculations are submitted to show that nitrogen crop usage rates based on plant-available nitrogen have not been
exceeded for the crop schedule submitted.
b. The correction factor for nitrogen losses shall be determined for the method of application by the following
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or from other credible sources for nitrogen volatilization correction factors.
Knifed in or soil injection of liquids 0.98
Surface-apply liquid or dry with incorporation within 24 hours 0.95
Surface-apply liquid or dry with incorporation after 24 hours 0.80
Surface-apply liquids with no incorporation 0.75
Surface-apply dry with no incorporation 0.70
Irrigated liquids with no incorporation 0.60
c. Nitrogen-based application rates shall be based on the optimum crop yields as determined in 65.17(6) and
crop nitrogen usage rate factor values in Table 4 at the end of this chapter or other credible sources.
d. A nitrogen-based manure rate shall account for legume production in the year prior to growing corn or
other grass crops and shall account for any planned commercial fertilizer application.
65.17(19) Requirements for application of a phosphorus-based manure rate to a field.
a. Phosphorus removal by harvest for each crop in the crop schedule shall be determined using the optimum
crop yield as determined in 65.17(6) and phosphorus removal rates of the harvested crop from Table 4a at the
end of this chapter or other credible sources. Phosphorus crop removal shall be determined by multiplying
optimum crop yield by the phosphorus removal rate of the harvested crop.
b. Phosphorus removal by the crop schedule shall be determined by summing the phosphorus crop removal
values determined in 65.17(19)“a” for each crop in the crop schedule.
c. The phosphorus applied over the duration of the crop schedule shall be less than or equal to the phosphorus
removed with harvest during that crop schedule as calculated in 65.17(19)“b” unless additional phosphorus
is recommended by soil tests and Iowa State University extension publication PM 1688, “General Guide for
Crop Nutrient Recommendations in Iowa.”
d. Additional requirements for phosphorus-based rates.
(1) No single manure application shall exceed the nitrogen-based rate of the planned crop receiving the particular manure application.
(2) No single manure application shall exceed the rate that applies to the expected amount of phosphorus
removed with harvest by the next four anticipated crops in the crop schedule.
e. If the actual crop schedule differs from the planned crop schedule, then any surplus or deficit of phosphorus
shall be accounted for in the subsequent manure application.
f. Phosphorus in manure should be considered 100 percent available unless soil phosphorus concentrations are
below optimum levels for crop production. If soil phosphorus concentrations are below optimum levels for
crop production phosphorus availability, values suggested in Iowa State University extension publication PM
1811, “Managing Manure Nutrients for Crop Production” or other credible sources shall be used.

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590 - 1

NATURAL RESOURCES CONSERVATION SERVICE
CONSERVATION PRACTICE STANDARD

NUTRIENT MANAGEMENT
(Ac.)
CODE 590

DEFINITION

•
•
•
•

Managing the amount, source, placement,
form and timing of the application of plant
nutrients and soil amendments.

Land receiving nutrients shall be evaluated for
environmentally sensitive areas such as, but
not limited to:

PURPOSE
•

To budget and supply nutrients
production.

•

To properly utilize manure or organic byproducts as a plant nutrient source.

•

To minimize agricultural nonpoint source
pollution of surface and ground water
resources.

•

To protect air quality by reducing nitrogen
emissions (ammonia and NOx compounds)
and the formation of
atmospheric
particulates.

•

commercial fertilizer,
crop rotation,
soil nutrient availability,
and irrigation water.

for plant

•
•
•
•
•
•
•

perennial water bodies,
areas of concentrated flow,
surface inlets,
Karst topography,
wellhead protection areas,
flood plain,
coarse textured soils.

Soil and Tissue Sampling and Laboratory
Analyses (Testing)
At a minimum, obtain soil test
analyses for
phosphorus, potassium, and pH. All soil
samples shall be collect ed according t o Iowa
State University (ISU) for sampling methods
based on soil maps, management zones, or
grid sampling. See ISU PM 287 “Take a Good
Sample to Help Make Good Decisions.” The
minimum frequency for soil testing shall be
once during a four-year period for continuous
row crop or once during the cycle of other crop
rotations that consists of close grown crops
such as grasses and legumes. The sampling
frequency can be less frequent for
organic
matter, however no greater than
every 12
years.

To maintain or improve the
physical,
chemical and biological condition of soil.

CONDITIONS WHERE PRACTICE APPLIES
This practice applies to all lands where plant
nutrients and soil amendments are applied.
CRITERIA
General Criteria Applicable to All Purposes
A nutrient management plan for nitrogen,
phosphorus, and potassium shall be
developed that considers all potential sources
of nutrients including, but not limited to:
• legume credits,
• animal manure and organic byproducts,
• waste water,

Use of the Late Spring Nitrate Test and Fall
Corn Stalk Test is encouraged in determining
rates of nitrogen and/or evaluating the nitrogen
management program. See ISU publications
PM-1714
“Nitrogen
Fertilizer

Conservation practice standards are review ed periodically and updated if needed. To obtain
the current version of this standard, contact
your Natural Resources Conservation Service
State Office or visit the electronic Field Office Technical Guide.

31

NRCS, IA
December 2008

O-74
590 - 2
Recommendations for Corn in Iowa” and PM
1584 “Corn Stalk Test to Determine Nitrogen”.

All nutrient values for phosphorus and
potassium should be expressed in pounds
P2O5 and K2O.

All soil tests shall be analyzed by a soil test lab
that is certified according to Iowa Department
of Agriculture and Land Stewardship (IDALS)
soil test lab certification standards. See ISUExtension
publication,
PM-1310 (rev)
"Interpretation of Soil Test Results. and PM1688 “A General Guide for Crop Nutrient and
Limestone Recommendations in Iowa.”

of

Phosphorus and potassium application for
crop and forage production (including non-crop
areas) shall be based on
soil test results.
Phosphorus and potassium additions shall not
exceed crop removal rates
when soil test
levels are optimum or above unless specified
under “Additional Criteria Applicable to Manure
and Organic By-Products or Biosolids Applied
as a Plant Nutrient Source”.

Nutrient Application Rates
Nutrient application includes form, source,
amount, timing and method of application on
each field. Plant nutrients may be applied as
broadcast, starter, surface band other than
starter, or injected
band applications.
Nutrients shall be applied to achieve realistic
production goals, while minimizing
nitrogen
and/or phosphorus movement to surface
and/or ground waters.

Commercial Nitrogen:
The amount of nitrate-nitrogen that moves
below the crop root zone is directly related to
nitrogen application rate. Therefore, overapplication in an attempt to produce unrealistic
yields or offset anticipated losses shall
be
avoided.
No fall application of commercial nitrogen shall
be made with the following exceptions:

All commercial nutrient applications shall be
based on ISU recommendations for the soil
type and crop to be grown. Use the most
recent publications.
See ISU-Extension
Publications PM1714 “Nitrogen Fertilizer
Recommendations for Corn in Iowa”, PM-1688
“General
Guide for Crop Nutrient
Recommendations in Iowa”, and
PM 869
“Fertilizing Pasture”. Unless specific nutrient
content for animal manure has been obtained
through sample analysis, the nutrient value of
animal manures will be estimated using
the
Agricultural
Waste Management
Field
Handbook (AWMFH), Chapter 4.

• Anhydrous ammonia if: (1) mid-day soil
temperatures, at 4”soil depth, is not
greater than 50 oF and trending lower;
(2) soil moisture conditions are
conducive to proper application and
sealing and (3) soil texture conditions
favor the retention of applied nitrogen.
• Application of nitrogen associated with
products that contain phosphorus
and/or potassium.
• Nitrogen associated with the production
of winter grains.

All nutrient applications shall be based
on
realistic yield potential for the field. Guidance
for estimating realistic yield
potentials is
outlined in ISU-Extension Publication PM-1268
(rev) "Establishing Realistic Yields." Realistic
yield potentials can be established based on
soil productivity information, historical yield
data, climatic conditions, level of management
and/or local research on similar soils, cropping
systems, and soil and
manure/organic byproducts tests. For new crops or varieties,
industry yield recommendations may be used
until documented yield information is available.

For more information consult Iowa State
University website on nitrogen management.
http://extension.agron.iastate.edu/soilfertility/nu
trienttopics/nutrienttopics.html
Where the Late Spring Nitrate Test is not
applicable, use the general recommendations
for nitrogen found in Iowa State Publications
PM-1714
“Nitrogen Fertilizer
ISU
Recommendations for Corn in Iowa”, ISU PM869 “Fertilizing Pasture”, ISU PM-1584
“Cornstalk Testing to Evaluate Nitrogen
Management”.

Phosphorus and Potassium.

NRCS, IA
December 2008
32

O-75
590 - 3
leaching, and volatilization losses.

All nutrient additions shall be
adjusted for
contributions from legumes, manure or other
organic nutrient sources.

•

Legume contributions are shown in
ISU
Publication PM-1714 “Nitrogen
Fertilizer
Recommendations for Corn in Iowa”.

Nutrients and organic nutrient sources shall
not be surface applied to frozen, snow covered
ground, or saturated soil if a potential risk for
runoff exists. A potentia l risk for runoff exis ts
on slopes greater than 5% unless erosion is
controlled to soil loss tolerance levels (“T”) or
less. Manure may be surface applied to
frozen, snow covered or saturated ground if a
potential risk for runoff exists only under one of
the following conditions.

Soil pH shall be maintained at levels shown in
ISU Publication PM-1688 “General Guide for
Crop Nutrient Recommendations in Iowa”. All
recommendations are based on Effective
Calcium Carbonate Equivalents (ECCE).
For soil tests requiring less than 2000 pounds
per acre ECCE, the lime requirement may be
waived.
Application equipment for fertilizers and
manure shall be calibrated at least annually to
determine actual applied rates. After
calibration, adjustments can be made in the
application process to meet the planned or
intended rates.

Nutrient Application Timing

On an emergency basis.

• Area of application.
• Other requirements such as runoff
control as indicated through the use of
the Iowa Phosphorus Index assessment
tool

Application methods to reduce the risk of
nutrient transport to surface and ground water,
or into the atmosphere shall be employed.

Conservation Management Unit (CMU) Risk
Assessment

To minimize nutrient losses:

Nutrients shall be applied considering
the plant growth habits, irrigation
practices, and other conditions so as
to maximize availability to the plant
and minimize the risk of
runoff,

o

• Rates of application.

Nutrient Application Methods

•

Where manure storage capacity is
insufficient and failure to surface
apply creates a risk of an
uncontrolled release of manure.

• Under what circumstances the manure
may be applied to frozen,
snow
covered, or saturated ground. (Ex:
storage capacity exceeded).

Timing and method of
nutrient application
(particularly nitrogen) shall correspond as
closely as possible with plant nutrient uptake
characteristics, while considering
cropping
system limitations, weather and climatic
conditions, risk assessment tools, (e.g., Pindex) manure storage capacity and field
accessibility.

Apply nutrient materials uniformly to
application area(s).

o

Manure surface applied to frozen,
snow
covered, or saturated ground shall be based
shall
on a manure disposal plan. That plan
include:

All specifications will be consistent with
federal, state, and local regulations.

•

Nutrient applications associated with
irrigation systems shall be applied in a
manner that prevents or
minimizes
resource impairment.

In areas with identified or designated nutrient
related water quality impairment, a CMU
(which is defined as a portion of a field, field,
group of fields, or other land units of the same
land use and having similar treatment needs
and management plans) shall be assessed for
the potential phosphorus transport risk from
the area. See Agronomy Technical Note 25,

NRCS, IA
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33

O-76
590 - 4
existing animal feeding operations utilizing
similar design and management as the
proposed animal feeding operation.

Iowa Phosphorus Index.
Any one of the following threshold factors will
trigger CMU risk assessment:
•

The CMU is located in a watershed
directly draining into waters identified
in the Iowa Department of
Natural
Resources (DNR) Iowa Integrated
Report as impacted by phosphorus.
http://wqm.igsb.uiowa.edu/wqa/303d.h
tml

•

Manure or organic by-products
applied

•

Soil loss exceeds the tolerable level

•

The average soil test phosphorus level
in the very high range as shown in ISU
Publication PM-1688 “General Guide
for Crop Nutrient Recommendation in
Iowa”.

For additional information on manure and
other organic nutrient management refer to
Standard and Specificati on Waste Utilization
(633) and the Agricultural Waste Management
Field Handbook.
Biosolids (sewage sludge) shall be applied in
accordance with USEPA regulations. (40 CFR
Parts 403 (Pretreatment) and 503 (Biosolids)
and other state and/or local regulations
regarding the use of biosolids as a nutrient
source.

are

Manure and Organic By-Product Nutrient
Application Rates
Planned application rates of nitrogen
and
phosphorus shall be determined based on the
following guidance:

Additional Criteria Applicable to Manure
and Organic By-Products or Biosolids
Applied as a Plant Nutrient Source

A. Nitrogen Application.
When
determining
allowable nutrient
application rates from manure or other organic
sources, nitrogen may be applied based on
crop nitrogen needs for that crop year. This
may allow application of more phosphorus and
potassium than required by the
crop. This
practice may continue as long as the risk of
phosphorus moving to surface waters based
on the Iowa Phosphorus Index is very low, low
or medium.

When animal manures or organic by-products
are applied, the Iowa Phosphorus Index will be
used as the risk assessm ent tool to evaluate
the potential for phosphorus transport from the
CMU and to adjust the amount, placement,
form and timing of application of phosphorus
sources.
Manure shall be analyzed for nutrient content
of total nitrogen, phosphorus and potassium,
percent moisture, and or percent solids. This
analysis shall be done at least annually for
each different source of manure being
generated at the animal
feeding operation.
Methods for sampling manure are discussed in
ISU Publication PM-1558 “How to Sample
Manure for Nutrient Analysis”.

When the plan is being implemented on a
phosphorus standard, manure or other organic
by-products shall be applied at rates
consistent with the phosphorus standard. In
such situations, an additional nitrogen
application from nonorganic sources may be
required to supply the recommended amounts
of nitrogen.

In planning for new animal feeding operations,
acceptable “book values” for the
nutrient
content and volume of manure that are
recognized by the NRCS may be used for the
proposed animal feeding operation ( NRCS
Agricultural
Waste Management
Field
Handbook, Chapter 4). In
the alternative,
nutrient content and volumes for proposed
animal feeding operations may be based on
historic nutrient content and volumes from

Manure or other organic by-products may be
the
applied on legumes at rates equal to
estimated removal of nitrogen in the harvested
portion of the crop that is removed from the
field in that growing season.
B. Phosphorus Application.
When manure or other organic by-products are
of phosphorus
used, the planned rates

NRCS, IA
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O-77
590 - 5
application shall be determined with reference
to the Iowa Phosphorus
Index (Agronomy
Technical Notice 25). The Iowa Phosphorus
Index (Iowa PI) asse sses the potential for
phosphorus movement from a field to surface
water, and designates fields as very low risk,
low risk, medium risk, high risk, and very high
risk.
Conservation practices and/or
phosphorus management practices can be
adopted that reduce the risk of phosphorus
movement and may reduce the risk rating on
the field. See Agronomy Technical Notice 25,
Iowa Phosphorus Index.
•

If a field is rated very low risk, low risk,
or medium risk by the Iowa PI, the
application of manure or organic byproducts may be made based on the
nitrogen needs of the crop as set forth
in subpart A above.

•

If a field is rated in the
medium risk
category, planned conservation and
phosphorus management practices
should not increase the rating of the
field above the medium risk category.

•

If a field is rated high risk or very high
risk by the Iowa PI; Manure or organic
by-products may be applied to meet
the needs of the planned crop rotation
for
phosphorus
removal
if
conservation
practices
and/or
phosphorus management practices
are adopted to reduce the risk of
phosphorus movement.

•

Heavy Metal Monitoring
When sewage sludge or biosolids are applied,
the application of potential heavy metal
pollutants (including arsenic, cadmium,
copper, lead, mercury, selenium, and zinc) in
the soil shall be in accordance with the Iowa
Administrative Code (IAC) IA567—67 and
IAC567--121.
Additional Criteria to Improve the Physical,
Chemical and Biological Condition of the
Soil
Nutrients shall be applied and managed in a
manner that maintains or improves the
physical, chemical and biological condition of
the soil.
To the extent practicable nutrients shall not be
applied when the potential for soil compaction
and rutting is high.
CONSIDERATIONS
Considerations are items to be
considered
during the planning process, however, are not
a required component of
the nutrient
management plan.
The use of management activities
and
technologies listed in this section may improve
both the production
and environmental
performance of nutrient management systems.

Nitrogen application limits of Subpart A
above should not be exceeded.

The addition of these management activities,
when applicable, increases the management
intensity of the system and is recommended in
a nutrient management system.

C. Sensitive Areas.
Manure and other organic nutrient sources
shall not be applied to
the following areas
unless injected or incorporated
within 24
hours:
•

Within 200 feet of sinkholes, drainage
wells, or other direct conduits to the
groundwater.

•

Within 200 feet of lakes, ponds, or
other perennial water bodies.

During the peak flood periods (April,
May, June, July) on land that floods
more than once every 10 years.

Action should be taken to protect
National
Register listed and other
eligible cultural
resources.
Animal feeding operations requiring removal of
manure more frequently than annually should
consider taking samples more frequently (i.e.
seasonally or after material changes to feed
rations or other operational aspects of the
animal feeding operation that may impact the
nutrient content of the manure) .

NRCS, IA
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O-78
590 - 6
The nutrient budget should be reviewed
annually to determine if any changes
are
needed for the next planned crop.

application area. Application methods and
timing that reduce the risk of nutrients being
transported to ground and surface waters, or
into the atmosphere include:

For sites on which there are
special
environmental concerns, other sampling
techniques may be appropriate. These include
soil profile sampling for nitrogen,
PreSidedress Nitrogen Test (PSNT).
Additional practices to enhance the producer’s
ability to manage manure effectively include
modification of the animal’s diet to reduce the
manure nutrient content, or utilizing
manure
amendments that stabilize or tie-up nutrients.
Soil test information should be no older than
one year when developing new plans,
particularly if animal manures are to be used
as a nutrient source.
Excessive levels of some nutrients can cause
induced deficiencies of other nutrients.

•

Split applications of nitrogen to provide
nutrients at the times of maximum
crop
utilization,

•

Use stalk-test to minimize risk of over
applying nitrogen in excess of crop needs.

•

Avoid winter nutrient application for spring
seeded crops,

•

Band applications of phosphorus near the
seed row,

•

Incorporate surface applied manures or
organic by-products as soon as possible
after application to minimize nutrient
losses,

•

Delay field application of animal manures
or organic by-products if precipitation
capable of producing runoff and erosion is
forecast within 24 hours of the time of the
planned application.

•

On soils with high permeability (greater
than 2 inches per hour through the 5 foot
profile), apply nitrogen using split spring
preplant/sidedress, at planting/sidedress
or sidedress applications to provide
distribution of nutrients at a time when
plants will utilize the nutrients.

•

Limit the application rate of liquid materials
applied to not exceed the soil infiltration
rate, to minimize ponding, to avoid runoff,
and to minimize loss to
subsurface tile
drains.

•

When applying manure to legume crops,
limit the crop available nitrogen application
to 125 pounds of nitrogen per acre.

If increases in soil phosphorus levels are
expected, consider a more frequent (annual)
soil testing interval.
To manage the conversion of nitrogen in
manure or fertilizer, use products or
materials (e.g. nitrification inhibitors,
urease inhibitors and slow or controlled
release fertilizers) that more closely match
nutrient release and availability for plant
uptake. These materials may improve the
nitrogen use efficiency (NUE) of the
nutrient management system by reducing
losses of nitrogen into water and/or air.
Considerations to Minimize Agricultural
Nonpoint Source Pollution of Surface and
Ground Water
Erosion control and runoff reduction practices
can improve soil nutrient and water storage,
infiltration, aeration, t ilth, diversity of soil
organisms and protect or improve water and
air quality (Consider installation of one or more
NRCS FOTG, Section IV –
Conservation
Practice Standards).

Considerations to Protect Air Quality by
Reducing Nitrogen and/or Particulate
Emissions to the Atmosphere
In areas with an identified or designated
nutrient management related air quality
concern, any com ponent(s) of nutrient
management (i.e., amount, source, placement,
form, timing of application) identified by risk

Cover crops can effectively utilize and/or
recycle residual nitrogen.
Apply nutrient materials uniformly to the

NRCS, IA
December 2008
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O-79
590 - 7
assessment tools as a potential source of
atmospheric pollutants should be adjusted, as
necessary, to minimize the loss(es).

Nutrient applications associated with irrigation
systems should be applied in accordance with
the
requirements
of Irrigation Water
Management (Code 449).

When tillage can be performed,
surface
applications of manure and fertilizer nitrogen
formulations that are subject to volatilization on
the soil surface (e.g., urea) should be
incorporated into the soil within 24 hours after
application.

CAFO operations seeking
permits under
USEPA regulations (40 CFR Parts 122
and
412) should consult with their respective state
permitting authority for additional criteria.

When manure or organic by-products are
applied to grassland, hayland, pasture or
minimum-till areas the rate, form and timing of
application(s) should be managed to minimize
volatilization losses.

PLANS AND SPECIFICATIONS
Plans
and specifications for
nutrient
management shall be in keeping with this
standard and shall describe the requirements
for applying the practice to achieve its intended
purpose(s), using nutrients to achieve
production goals and to prevent or minimize
resource impairment.

When liquid forms of manure are applied with
irrigation equipment, operators should select
weather conditions during application that will
minimize volatilization losses.

Nutrient management plans shall include a
statement that the plan was developed based
on requirements of the current standard and
any applicable Federal, state, or
local
regulations, policies, or programs, which may
include the implementation of other practices
and/or management activities. Changes in any
of these requirements may necessitate a
revision of the plan.

Operators should handle and apply poultry
litter or other dry types of animal manures
when the potential for wind-driven loss is low
and there is less potential for transport
of
particulates into the atmosphere.
Weather and climatic
conditions during
manure or organic by-product application(s)
should be recorded and maintained
in
accordance
with
the operation and
maintenance section of this standard.

The following components shall be included in
the nutrient management plan:

Odors associated with the land application of
manures and organic by-products can be
offensive to the occupants of nearby homes.
When possible, application of these materials
upwind of occupied structures when residents
are likely to be home (evenings,
weekends
and holidays) should be avoided.
When applying manure with irrigation
equipment, modifying the
equipment can
reduce the potential for volatilization of
nitrogen from the time the manure leaves the
application equipment until it reaches
the
surface of the soil (e.g., reduced pressure,
drop down tubes for center pivots). Nitrogen
volatilization from manure in
a surface
irrigation system should be reduced when
applied under a crop canopy.
When planning nutrient applications and tillage
operations, encourage soil carbon buildup
while discouraging greenhouse gas emissions
(e.g., nitrous oxide N2O, carbon dioxide CO2).

•

aerial site photograph(s) or site map(s),
and a soil survey map of the site,

•

location of designated sensitive areas or
resources and the associated, nutrient
management restriction,

•

current and/or planned plant
sequence or crop rotation,

•

results of soil, water, manure and/or
organic by-product sample analyses,

•

results of plant tissue analyses, when used
for nutrient management,

•

realistic yield goals for the crops,

•

complete nutrient budget for nitrogen,
phosphorus, and potassium for the crop
rotation or sequence,

•

listing and quantification of all nutrient
sources,

•

CMU

production

specific recommended nutrient

NRCS, IA
December 2008
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O-80
590 - 8
application rates, timing, form, and method
of application and incorporation, and
•

reasons for the differences.
•

guidance for implementation, operation,
maintenance, and recordkeeping.

If increases in soil phosphorus levels are
expected, the nutrient management plan shall
document:
•

the soil phosphorus levels at which it may
be desirable to convert to
phosphorus
based planning,

•

results of appropriate risk assessment
tools to document the relationship between
soil phosphorus levels and potential for
phosphorus transport from the field,

•

the potential for soil phosphorus drawdown
from the production and harvesting
of
crops, and

•

management activities or techniques used
to reduce the potential for phosphorus
loss.

OPERATION AND MAINTENANCE
The owner/client is responsible for safe
operation and maintenance of this practice
including all equipment. Operation
and
maintenance addresses the following:
•

periodic plan review to determine if
adjustments or modifications to the plan
are needed. As a minimum, plans will be
reviewed and revised with each soil test
cycle.

•

significant changes in animal
numbers
and/or feed management will necessitate
additional manure sampling and analyses
to establish a revised
average nutrient
content.

•

calibration of application equipment to
ensure uniform distribution of material at
planned rates.

•

documentation of the actual rate at which
nutrients were applied. When the actual
rates used differ from the recommended
and planned rates, records will indicate the

o

Soil, plant tissue, water, manure, and
organic by-product analyses resulting
in recommendations for nutrient
application,

o

quantities, analyses and
nutrients applied,

sources of

o

dates and method(s) of
applications,

nutrient

o

weather conditions and general soil
moisture (e.g. wet, damp, dry) at the
time of application; lapsed time
to
manure incorporation, rainfall
or
irrigation event.

o

crops planted, planting and harvest
dates, yields, and
crop residues
removed,

o

dates of plan review, name of
reviewer, and recommended changes
resulting from the review.

Records should be maintained for five years;
or for a period longer than five years if required
by other Federal, state or local ordinances, or
program or contract requirements.
Workers should be protected from and avoid
unnecessary contact with plant nutrient
sources. Extra caution must be taken when
handling ammoniacal nutrient sources, or
when dealing with organic wastes stored in
unventilated enclosures.
Material generated from cleaning
nutrient
application equipment should be utilized in an
environmentally safe manner. Excess material
should be collected and stored or field applied
in an appropriate manner.

protection of fertilizer and organic byproduct storage facilities from weather and
accidental leakage or spillage.

•

Maintaining records to document plan
implementation. As applicable, records
include:

Nutrient containers should be recycled in
compliance with state and local guidelines or
regulations.

NRCS, IA
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O-81
590 - 9

REFERENCES

The following publication is available on the
NRCS web site at
http://policy.nrcs.usda.gov/viewerFS.aspx?hid=21430

These publications are available at County
Extension Offices; Ex tension Distribution
Center, Printing Building, Iowa State
University, Ames, IA 50011; and several are
available on the ISU Publications Home page
at
http://www.extension.iastate.edu/Pages/pubs/.
•
•
•
•
•
•
•
•
•
•

•
•

•

Agricultural Waste Management Field
Handbook

The following Standard on Manure Production
from the
and Characteristics is available
American Society of Agricultural and Biological
Engineers.
http://asae.frymulti.com/standards.asp

ISU PM-1310 “Interpretation of
Soil
Test Results”
ISU PM-287 “Take a Good Sample to
Help Make Good Decisions”
ISU PM-1714 “Nitrogen Fertilizer
Recommendations for Corn in Iowa”
ISU
PM-2015
“Concepts and
Rationale for Regional Nitrogen Rate
Guidelines for Corn”
ISU PM-1688 “General Guide for Crop
Nutrient Recommendations in Iowa”
ISU PM-869 “Fertilizing Pasture”
ISUPM-1268(rev)
“Establishing
Realistic Yields”
ISU PM-1584 “Cornstalk Testing to
Evaluate Nitrogen Management”
ISU PM-1436 “Nitrogen Fertilizer
Management for Northeast Iowa”
ISU PM-569 “Warm-Season Grasses
for hay and Pasture”
ISU PM-1558 “How to Sample Manure
for Nutrient Analysis”
ISU
PM-1941
“Calibration and
Uniformity of Solid Manure Spreaders”
ISU PM-1948 “Calibrating Liquid Tank
Manure Applicators”

•

ASABE D384.2 MAR2005

The following publications are available at the
Iowa Conservation Partners Home page at:
http://www.ia.nrcs.usda.gov.
• Iowa Technical Note 25, Iowa Phosphorus
Index
• Background and Basic Concepts of the
Phosphorus Index
• Phosphorus Index Calculator
(Excel
Spreadsheet)
• Waste Utilization Standard (633)

NRCS, IA
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O-82

Nitrogen Fertilizer
Recommendations for
Corn in Iowa
This pamphlet replaces all earlier guidelines
for using the late-spring test for soil nitrate
and all previous nitrogen fertilizer recommendations based on corn yield goals and
credits for N supplied by legumes and animal manures. Recommendations concerning applications of animal manures are
provided in Pm-1596a, Managing manure
nutrients for crop production.

N

itrogen fertilization is essential for profitable corn production. It also is a major
cost of production and can contribute to
degradation of the environment. The economic and
environmental costs of N fertilization are more
important than in the past, and they are likely to
become even more important in the future. These
costs provide compelling reasons for intensifying
efforts to improve N management practices.
The late-spring test for soil nitrate is a new technology that enables site-specific assessments of
plant-available N just before the crop begins rapid
uptake of N. Use of this test should help corn
producers manage N to increase their profits while
reducing environmental degradation. All producers are encouraged to use this test, but the way the
test is used depends on whether or not the producer exercises the option for in-season fertilization (i.e., N applications after corn plants are 6
inches tall).
Producers who apply all their N before emergence
of the crop (i.e., before planting, at planting, soon
after planting) should apply N at rates indicated in
Table 1 and use the late-spring test to evaluate their
N management. Select rates within the ranges
given by considering price for fertilizer, expected
price for grain, supply of subsoil moisture, and
feedback given by the end-of-season cornstalk test
in previous years. If price and yield outlook are
favorable, select the upper part of the range; if
unfavorable, select the lower part of the range.

Table 1. Rates of N usually needed if all N is applied
preplant or before crop emergence (option for inseason application of N not exercised).
Crop category
N rate (lb. N/acre)
Corn on recently manured soils
0-90
Corn after established alfalfa
0-30
2nd-year corn after alfalfa
0-60
Other corn after corn
150-200
Corn after soybean (no manure)
100-150
Additional information is provided on page 4.

Producers who use the option for in-season
fertilization (i.e., split applications or all applied
after corn plants are 6 inches tall) should apply N
at rates indicated in Table 2 and then use the latespring test to estimate additional amounts of N
needed. Rates within the range given should be
selected based on the extent to which the producer
wants to rely on in-season fertilization, amounts of
rainfall during the previous six months, and
feedback given by the end-of-season cornstalk test
in previous years.
Application of some N before crop emergence is
desirable to avoid the possibility of early-season
deficiencies and to reduce risks associated with
weather conditions that prevent in-season fertilization. Application of all N before planting, however,
reduces the ability to adjust N rates for the effects
of spring weather on amounts of N supplied by the
soil or the amounts lost during spring rainfall. Use
of the late-spring test over a period of years provides information that can be used to optimize preemergence applications of N.
Table 2. Rates of N to apply before crop emergence
if the option for in-season fertilization is exercised.
Category
N rate (lb. N/acre)
Corn on recently manured soils
0-30
Corn after established alfalfa
0-30
2nd-year corn after alfalfa
0-30
Other corn after corn
50-125
Corn after soybean (no manure)
0-75
The 30-lb. rates could be applied as a starter.

Pm-1714 | May 1997
LEOPOLD CENTER

40

O-83

Soil Sampling and Testing
Time of Soil Sampling
Soil samples should be collected when corn plants
are 6 to 12 inches tall (measured from the ground
surface to the center of the whorl).

area. The third is collected one-quarter of the
distance between any two corn rows after moving
to another part of the test area. The process is
continued until the eighth core is collected seveneighths of the distance between any two corn rows.

Selecting Test Areas
Soil samples should be collected within several test
areas that are 1 to 10 acres and seemingly uniform
with respect to soil characteristics and management
histories. Care should be taken to avoid unusual
spots (e.g., sites of old barnyards, feedlots, or
manure piles, field edges or ends where fertilizer
applicators may have made skips or double applications, abnormal patches of growing weeds or plant
residues, or small areas where corn plants suggest
differences in N availability).
The optimal number of test areas per farm should
be expected to vary with many factors. First-year
users of the test should consider testing about five
areas for the first 100 acres and two more areas for
each additional 100 acres. Information gathered in
the first year can be used to help select future
sampling strategies that are appropriate for a
particular farm.

Depth of Soil Sampling

The soil from all cores should be crushed and
thoroughly mixed before a subsample is removed
for analysis.

Handling and Shipping Soil Samples
Moist soil samples should be protected from
temperatures above 75°F and should be refrigerated if they cannot be analyzed within two days.
Mailing usually poses no problem if the samples
are without refrigeration for no more than two
days. Assume that soil testing laboratories will
protect the samples as soon as they are received.
Soil samples expected to be without refrigeration
for more than two days should be dried as soon as
possible. Samples can be air-dried by spreading in
a thin layer on paper — a fan will accelerate
drying. Samples can be dried in an oven provided
the temperature does not exceed 250° F.

Samples collected for the late-spring soil test must
be representative of the surface foot of soil.

Soils that are extremely wet or muddy should not
be sampled. Incorrect results will be obtained if
water “drips” from the samples.

Number of Cores per Sample

Soil Analysis

Soil samples analyzed for this test should be
derived from at least 16 to 24 cores. Care should
be taken to ensure that the soil samples are collected in a manner that is not biased by the presence of corn rows or bands of fertilizer. At least 24
cores should be collected if anhydrous ammonia
was applied for the present crop.

The late-spring test is based on concentrations of
nitrate-nitrogen (NO-3-N) in the soil sample. Most
soil testing laboratories can perform this analysis.
Nitrate concentrations also can be measured on the
farm by using commercially available kits.

Sampling bias can be minimized by collecting soil
samples in “sets of eight” cores that have various
assigned positions relative to corn rows. By this
method, the person doing the sampling moves in a
random pattern within the test area to select
approximate positions for collecting cores. Each
time a core is collected, however, its exact position
is selected relative to the two nearest corn rows.
The first core is collected in a row. The second is
collected one-eighth of the distance between any
two rows after moving to another part of the test

This pamphlet expresses nitrate concentrations in
terms of ppm nitrate-N (parts of N per million parts
of dry soil), which is the same as ppm N as nitrate.
Concentrations expressed as ppm nitrate must be
multiplied by 0.23 to be converted to ppm nitrate-N.
Users of the soil test should be alert to the possibility
of incorrect results on individual samples. Errors can
occur during collection, handling, and analysis of
samples. The impact of such errors can be substantially reduced by observing trends in soil test results
and using caution when making recommendations
on results that deviate from these trends.
41

O-84

Soil Test-based N Recommendations
Manured Soils, First-year Corn After Alfalfa,
and Second-year Corn After Alfalfa
Soils that have received recent applications of
animal manures or have decaying sods with alfalfa
roots seem to mineralize more plant-available N
after the time of soil sampling than do other soils.
These soils, therefore, are treated as a separate
category when making N fertilizer recommendations.
These recommendations are given in Table 3.
The first step for making recommendations from
Table 3 is to decide whether the top half of the
table or the lower half of the table best describes
the current prices for grain and fertilizer.
Table 3. Nitrogen fertilizer recommendations for
manured soilsa and corn after alfalfa.
Grain and
Soil test
Recommended N rate
fertilizer
nitrate
Excessb
Normal
prices
Rainfall
Rainfall
ppm N
--------- lb. N/acre---------Unfavorable
(1 bu buys
7 lb. of N)

0-10
11-15
16-20
> 20

90
0
0
0

90
60
0c
0

Favorable
(1 bu buys
15 lb. of N)

0-10
90
90
11-15
60
60
16-25
0
30
> 25
0
0
a
A field should be considered manured if animal
manures were applied with a reasonable degree of
uniformity since harvest of the previous crop or in 2
of the past 4 years.
b
Rainfall should be considered excess if rainfall in
May exceeded 5 inches.
c
Addition of 30 lb. N/acre may have no detectable
effects on profits, but producers could reasonably
elect to apply this rate.

The second step is to decide whether the “excess
rainfall” column or the “normal rainfall” column of
the table best describes weather conditions before
the soils were sampled.
The third step is to use the results of the soil test
to select the appropriate N rate specified. Interpolation between specified N rates is appropriate
when site conditions fall between those given.

42

Corn After Soybean and Corn After Corn
The first step in making a fertilizer recommendation for this crop category is to select a critical
concentration for nitrate (i.e., the concentration
that distinguishes between adequate and inadequate supplies of available N). A critical concentration of 25 ppm-N is appropriate in absence of
additional information.
The second step is to adjust the critical concentration if excess rainfall occurred at the site shortly
before the soils were sampled. Reducing the critical
concentration by 3 to 5 ppm is advised if rainfall is
more than 20 percent above normal amounts
between April 1 and time of soil sampling.
The third step is to estimate fertilizer needs by
subtracting the concentration of soil-test nitrate
(ppm-N) from the chosen critical concentration
(ppm-N). This value is then multiplied by 8. A
factor of 8 is used because studies have shown that
it usually takes about 8 lb. of N/acre before planting to increase soil-test nitrate-N by 1 ppm.
Examples: A soil test of 15 ppm and a critical
concentration of 25 ppm results in a recommendation of 80 lb. of N per acre to be applied.
(25 ppm - 15 ppm) x 8 = 80 lb. N/acre needed
A soil test of 35 ppm and a critical concentration of
25 ppm indicates that the soil already has approximately 80 lb. of N more than needed.
(25 ppm - 35 ppm) x 8 = -80 lb. N/acre needed.

O-85

Additional Information

Yield Goals and Nitrogen Credits

Yield goals (or potentials) are no longer used when
making N fertilizer recommendations because
research has shown no relationship between
optimal rates of N fertilization and yields at these
optimal rates.
The use of legume and(or) manure credits has been
eliminated. The effects of those sources of N are
addressed by giving recommendations for separate
categories.

Addressing Variability
The best rate of N fertilization for corn varies
greatly with year and location. This variability is
caused by complex interactions of soil factors,
management practices, and weather. Time and
method of N application are important because
they influence amounts of N lost before it can be
used by the corn.
Great variability in optimal rates of N fertilization
is a problem because the best rates across a wide
range of conditions usually are not best for most
individual sites in a given year. This problem was
unavoidable in the past, but advances in technology offer new opportunities for site-specific management of N.
Users of the soil test should expect much greater
variability in amounts of N supplied by animal
manures and legumes than would be expected from
commonly used methods to calculate N credits.
Research has shown that this variability should be
considered a reason for using the soil test rather
than evidence that the test is not reliable.

Reliability of the Soil Test
The soil test should be considered only a tool for
estimating availability of N in soils. Like any tool,
the usefulness of this test varies with the skill of
the user. First-time users are encouraged to
experiment with the test in small areas before using
it to guide fertilization on all their fields.
Recommendations for using the soil test are intended to maximize profits for the producer when
used across many sites and years. Because many
factors that influence fertilizer needs at a specific
site and year happen after the soils are tested, the
soil test should not be expected to be a perfect

predictor of fertilizer needs. Use of the soil test is
recommended because it is more reliable than
other methods of estimating N fertilizer needs.
Moreover, it is likely that the reliability of the
soil test can be improved as new knowledge is
acquired.

Where Caution is Required
The soil test may underestimate amounts of plantavailable N when (1) nitrification inhibitors or
urease inhibitors are applied with fertilizers, (2)
more than 150 lb. N/acre are applied as anhydrous
ammonia, and (3) more than 150 lb. N/acre are
applied as injected manure.
Use of the soil test on sandy soils may require
deeper sampling if fertilizers are applied before
crop emergence and unusually large amounts of
rainfall occur between fertilization and sampling.
There are relatively few sandy soils in Iowa.

End-of-season Cornstalk Testing
Users of the late-spring test are encouraged to use
the end-of-season cornstalk test, which is described
in ISU Extension factsheet, Cornstalk Testing to
Evaluate Nitrogen Management, Pm-1584. The endof-season test essentially asks if the corn crop had
too little, too much, or optimal amounts of N.
The resulting information can be used to evaluate
the reliability of the soil test or any other system of
making N recommendations. When used over a
period of several years, information provided by
the cornstalk test can be used to help select rates of
N application that are most appropriate for the soil
factors and management practices that make sites
differ in N fertilizer requirements.
Prepared by A.M. Blackmer and R.D. Voss, professors; and A. P. Mallarino, assistant professor, ISU
Department of Agronomy.
. . . and justice for all
The Iowa Cooperative Extension Service’s programs and policies are
consistent with pertinent federal and state laws and regulations on
nondiscrimination. Many materials can be made available in alternative
formats for ADA clients.
Issued in furtherance of Cooperative Extension work, Acts of May 8 and
June 30, 1914, in cooperation with the U.S. Department of Agriculture.
Stanley R. Johnson, director, Cooperative Extension Service, Iowa State
University of Science and Technology, Ames, Iowa.
File: Agronomy 8-5

43

44

PM 1688 Reviewed and Reprinted September 2008

A General Guide
for Crop Nutrient and
Limestone Recommendations
in Iowa

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Table 7. Phosphorus and potassium recommendations
for sunflower production _______________________________________________ 6

Table 6. Phosphorus and potassium recommendations
for wheat production __________________________________________________ 5

Table 5. Phosphorus and potassium recommendations
for oat grain and straw production _______________________________________ 5

Table 4. Phosphorus and potassium recommendations
for soybean production ________________________________________________ 4

Table 3. Phosphorus and potassium recommendations
for corn grain production ______________________________________________ 4

Method of Application ______________________________________________ 3

Table 2. The nutrient content of harvested crops used to calculate
nutrient removal and recommended amounts of P2O5 and K2O
for optimum soil test category___________________________________________ 2

Phosphorus and Potassium Recommendations ___________ 2

Table 1. Interpretation of soil test values for phosphorus (P) determined
by Bray P1, Mehlich-3, or Olsen extractants and potassium (K) determined
by ammonium acetate or Mehlich-3 extractants for surface soil samples
(6- to 7-inch deep cores) _______________________________________________ 2

Soil Test Categories ____________________________________ 1

Soil Test Procedures ____________________________________ 1

Introduction ____________________________________________ 1

Contents

Figure 1. Map of Iowa delineating the 21 principal soil association
areas (letters) and the 12 major soil areas (numbers). ______________________ 18

Table 15. Subsoil phosphorus and potassium levels that are to be
used to determine phosphorus and potassium nutrient recommendations
for the major soil series in each of the 12 major soil areas in Iowa. _________ 10–17

Soils __________________________________________________ 10

Table 14. Lime recommendations, based on SMP Buffer Test, are given
in pounds of pure fine calcium carbonate (CaCO3) to increase soil pH
from its present level to pH 6.5 or 6.9 for the depth of soil to be neutralized _____ 9

Limestone Recommendations ___________________________ 9

Table 13. Zinc recommendations for corn and sorghum production ___________ 9

Micronutrient Recommendations ________________________ 9

Table 12. Phosphorus and potassium recommendations
for bluegrass dominant pasture __________________________________________ 8

Table 11. Phosphorus and potassium recommendations
for tall cool-season grasses, warm-season perennial grasses, and
sorghum-sudan hay and pastures ________________________________________ 8

Table 10. Phosphorus and potassium recommendations
for clover- and trefoil-grass hay and pastures _______________________________ 7

Table 9. Phosphorus and potassium recommendations
for alfalfa and alfalfa-grass hay and pastures _______________________________ 7

Table 8. Phosphorus and potassium recommendations
for corn silage or sorghum silage production _______________________________ 6

O-87

1  Iowa State University Extension

The soil tests for which interpretations
are given in this publication are the Bray
P1, Mehlich-3, and the Olsen tests for P,
the ammonium acetate and Mehlich-3
tests for K, the DTPA test for Zn, a water-soil slurry for soil pH, and the SMP
buffer method for lime requirement.
The Bray P1 test is not recommended
for soils with soil pH 7.4 or higher
(calcareous) because it often underestimates plant-available P in those soils
and can return false low values. Soil
test P interpretations in this publication
apply when a colorimetric method is

Soil Test Procedures

Nutrients applied to meet the recommended amounts may be from inorganic
sources, from manure, or both. Nutrient
contents of manures are most accurately
determined by laboratory analyses.

Phosphorus (P), potassium (K), zinc
(Zn), and lime recommendations based
on soil testing are provided in this publication for the major agronomic crops
grown in Iowa. Interpretation of soil test
values and nutrient recommendations
are based on soil samples taken to a 6to 7-inch depth. Research results from
long-term and short-term field experiments have been used to determine the
interpretation of soil test values and the
nutrient recommendations.

Introduction

46

Soil test numerical values are reported
as parts per million (ppm). Soil test
values for P and K have been classified
into interpretive categories designated
very low (VL), low (L), optimum (Opt),
high (H), and very high (VH). These
categories represent a decreasing probability of an economic yield response to
applied nutrients. The percentage of P

Soil Test Categories

used to measure the P extracted by the
Bray P1, Mehlich-3, and Olsen P tests.
These tests, and those for soil pH and
buffer pH, are among the tests recommended for the North Central Region
by the NCR-13 Regional Committee on
Soil Testing and Plant Analysis. These
and other tests are described in the
North Central Regional Publication 221
(Revised 1998), Recommended Chemical
Soil Test Procedures for the North Central
Region. In addition, soil test P interpretations are provided when an ICP
(inductively coupled plasma) analytical
method is used to measure the P extracted by the Mehlich-3 P test (Mehlich-3 ICP). All laboratory procedures
have some inherent variability and thus
soil test results should be viewed as a
potential range in values. The ranges in
variation for routine soil test results produced within a laboratory are expected
to be on the order of ±10% for soil test P
and K, and ±0.1 pH unit.
Soil test categories for the numerical
soil test values of P and K are given in
Table 1. The interpretation of P and K
soil test values into categories depends
on the nutrient demand of the crop to
be grown, the subsoil concentrations
of P and K, and the soil test value. The
interpretation of P soil test values for
wheat and alfalfa is different than for
the other agronomic crops indicating
that these two crops require a higher
soil P level in the surface soil for profitable production. The interpretation of P
soil test values for all crops other than
wheat and alfalfa, and K soil test values
for all agronomic crops, differs according to subsoil P and K levels of the soil
series.

and K applications expected on average
to produce a yield response within each
soil test category is 80% for very low,
65% for low, 25% for optimum, 5% for
high, and <1% for very high. Based on
input costs and expected yield increases,
the optimum category is the most profitable category to maintain over time. The
very high category indicates that the nutrient concentration exceeds crop needs,
and further additions of that nutrient
very seldom produce a profitable yield
response. Recommended applications
are structured so that over time soil tests
will move to the optimum category.

Subsoil P and K levels for soil series
with more than 5,000 acres and a corn
suitability rating (CSR) greater than
30 are given in Table 15 for each of the
major soil areas in Iowa that contain
the principal soil associations shown
in Figure 1. Subsoil levels do vary by
soil series but not by soil mapping units
within a soil series.

Subsoil P and K levels are determined
at the depth that provides the greatest
range of soil test values for each nutrient. Subsoil P is determined by
the Bray P1 soil test for samples taken
from the 30- to 42-inch depth. Subsoil
K is determined by the ammonium
acetate soil test for samples taken from
the 12- to 24-inch depth. Subsoil P is
designated low for subsoil test values
of 8 ppm or less and high for values of
9 ppm or more. Subsoil K is designated
low for subsoil test values of 50 ppm or
less and high for values of 51 ppm or
more. The effect of a high subsoil level
of P or K is to require a lower concentration of that nutrient in the surface
soil for optimum crop production.

General Guide for Crop Nutrient and Limestone Recommendations in Iowa

O-88

16–20
21–25
26–30
31+

00–10
11–14
15–17

18–20
21+

00–20
21–30
31–40
41–50
51+

Very low (VL)
Low (L)
Optimum (Opt)

High (H)
Very high (VH)

Very low (VL)
Low (L)
Optimum (Opt)
High (H)
Very high (VH)

High

Low

High

Subsoil K

2  Iowa State University Extension

The recommended amounts of P2O5 and
K2O are based on research conducted
in Iowa during many years. Applying
the recommended rates for the very low

00–50

00–10
11–20
21–30
31–40
41+

12–15
16+

00–30
04–70
08–11

06–10
11–15
16–20
21+

91–130
131–170
171–200
201+

000–900
71–110
111–150
151–180
181+

000–700

or Mehlich-3 K

Ammonium Acetate

47

and low soil test categories will result
in profitable crop responses in that year
and at the same time increase soil test
values after crop harvest because of significant residual effects from the applied
P and K.

00–15
16–25
26–35
36–45
46+

Mehlich-3 ICP

15–20
21+

00–5
06–10
11–14

Olsen P

09–15
16–20
21–30
31+

00–80

Phosphorus and
Potassium Recommendations

00–15

Low (L)
Optimum (Opt)
High (H)
Very high (VH)

Bray P1 or Mehlich-3 P

Very low (VL)

Relative level

Low

Subsoil P

All crops

- - - - - - - - - - - - - - - - - - - - - ppm - - - - - - - - - - - - - - - - - - - - -

alfalfa

Wheat,

All crops except
wheat, alfalfa

Table 1. Interpretation of soil test values for phosphorus (P) determined by
Bray P1, Mehlich-3, or Olsen extractants and potassium (K) determined
by ammonium acetate or Mehlich-3 extractants for surface soil samples
(6- to 7-inch deep cores).

category use default yield levels. These
can be adjusted to a field-specific yield.
The nutrient content per unit of yield
for Iowa agronomic crops is given in
Table 2.

ton
ton
ton
ton
ton
ton
ton
ton
ton
ton

Trefoil
Vetch
Smooth bromegrass
Orchardgrass
Tall fescue
Timothy
Perennial ryegrass
Sorghum-sudan
Switchgrass
Reed canarygrass

12.0
12.0
9.0
14.0
12.0
9.0
12.0
12.0
12.0
9.0

0.55
3.50
5.9
0.80
2.8
0.40
5.0
0.60
4.0
0.80
12.50
12.0

0.375

P2O5

35.0
47.0
47.0
68.0
66.0
32.0
34.0
38.0
66.0
47.0

1.25
8.0
25.0
1.50
9.9
1.00
33.0
0.30
25.0
0.70
40.0
35.0

0.30

K2O

*Nutrients in corn and soybean stover reflect content at plant maturity (dry matter based),
and will therefore be more representative of stover harvested immediately after grain harvest. Corn stover is an average content of all aboveground plant components except grain.
Soybean stover is nutrient content only of stems.

bu grain equivalent
ton, 65% H2O
ton
bu
ton
bu
ton
bu
ton
100 lb
ton
ton

bu

Unit of Yield

Corn silage
Corn silage
Corn stover*
Soybean
Soybean stover*
Oat and straw
Oat straw
Wheat
Wheat straw
Sunflower
Alfalfa
Red clover

Corn

Crop

Pounds per unit of yield

Table 2. The nutrient content of harvested crops used to calculate nutrient
removal and recommended amounts of P2O5 and K2O for optimum soil
test category.

The recommended P and K rates for the
optimum soil test category are based on
average nutrient removal in harvested
crop parts (grain, silage, straw, and
hay). The fertilization amounts shown
in the tables for the optimum soil test

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3  Iowa State University Extension

The recommendation tables provide
suggested P and K applications intended
for a single crop grown after soil sampling. Economic considerations suggest
that a new soil test should be planned
every two to four years for most crops.
For P and K applications after the initial
crop year and between soil testing
years, and for multi-year applications
planned for consecutive grain crops
(for example, multi-year application for
corn-soybean and corn-corn rotations),
adjustment should be made to the recommended annual amounts. Available
research data suggest that when recommended P and K amounts are applied to
soils that test in the very low category,
recommended amounts for the low
category can be applied to subsequent
crops until the next planned soil testing,
but not for more than three years. When
the recommended P and K amounts
are applied to soils that test in the low
category, recommended amounts for
the optimum category can be applied
to subsequent crops until the next
planned soil testing, but not for more
than three years. When soil tests are in
the optimum category, the crop removal
amount can be applied each year. For
grain crops, an amount equivalent to the
sum over two crop years can be applied

48

The optimum soil test category is the
most profitable to maintain. Phosphorus and K application in the high
category seldom produces a profitable
yield increase, and no recommendation is made for annual (one crop-year)
application. However, if the soil test is
in the lower part of the high range, a
multi-year application is planned for
grain crops (for example, consecutive
corn and soybean crops), and it will
be two to four years until the next soil
sampling, consider applying a partial
crop removal rate during that period to
ensure adequate nutrients for subsequent crops and to moderate soil test
decline. The very high soil test category
indicates that the nutrient concentration exceeds crop needs, and further
additions of that nutrient very seldom
produce a yield response. Therefore, no
application is recommended for the very
high category.

in one application. Annual P and K applications are recommended for silage
or forage crops to minimize excessive
nutrient removal when large nutrient
rates are applied at one time.

Method of Application
The recommended amounts for P and K
are based on yield responses to applications in many tillage systems—from
conventional-tillage to reduced-tillage
and no-tillage systems. Research has
shown that in most reduced-tillage
systems equivalent crop responses are
expected for broadcast, 22 band, and
deep band P and K applications. The
exceptions are for K in ridge-tillage
corn and soybean where bands placed
into the ridge provide higher yields
than broadcast, and K in no-tillage
corn where deep banding can produce
greater yield response than broadcast or
22 band placement. However, on average the no-tillage corn yield increase
Application of banded NP or NPK
starter fertilizer for corn in the high
soil test category may be advantageous
under conditions of limited soil drainage, cool soil, crop residues on the soil
surface, or late planting dates with fullseason hybrids. Placement of starter fertilizer with corn seed should be limited
to 10 pounds or less of N + K2O per acre
to reduce the risk of decreased plant
stand. If soils are sandy or dry, reduce
the amount of N + K2O by one-half. It
is recommended that no fertilizer be
placed in contact with soybean seed.

from deep K banding is not large and
may often not pay for the increased application costs.

O-90

75

0–15
0–10

100

Mehlich-3 ICP:
Low Subsoil P
High Subsoil P

Low

130
110

90
70

171–200
151–180

High

K2O to apply (lb/acre)
45
0
45
0

131–170
111–150

Optimum*

Potassium Soil Test (ppm)

Very Low

36–45
31–40

12–15

15–20

21–30
16–20

High

0
0

201+
181+

Very High

0

46+
41+

16+

21+

31+
21+

Very High

4  Iowa State University Extension
49

*The recommended amounts of P2O5 and K2O for the optimum soil test category are based
on approximate nutrient removal for the harvested yield. The amounts shown
in the table for the optimum soil test category are based on 150 bu corn grain per acre.
Nutrient removal amounts can be adjusted higher or lower for other yield levels. At the high
soil test category, banded NP or NPK starter fertilizer may be advantageous under conditions of limited soil drainage, cool soil, crop residues on the soil surface, or late planting
dates with full-season hybrids. None is recommended for the very high soil test category.
Recommendations for soils with a corn suitability rating (CSR) of 30 or less should be based
on expected crop yield and nutrient removal for soil test categories of optimum or lower.

Fine Textured
Sandy Textured

26–35
21–30

08–11

11–14

16–20
11–15

Optimum*

P2O5 to apply (lb/acre)
55
0

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

16–25
11–20

0–30

High Subsoil P

4–70

6–10

0–50

Olsen P:
Low Subsoil P

Low
9–15
6–10

Very Low

Bray P1 and Mehlich-3 P:
Low Subsoil P
0–80
High Subsoil P
0–50

Soil Test Category:

Phosphorus Soil Test (ppm)

Table 3. Phosphorus and potassium recommendations for corn grain
production.

Very Low

60

16–25
11–20

04–70

06–10

Low

120
100

90
85

171–200
151–180

High

K2O to apply (lb/acre)
75
0
75
0

131–170
111–150

Optimum*

0
0

201+
181+

Very High

0

46+
41+

16+

21+

31+
21+

Very High

*The recommended amounts of P2O5 and K2O for the optimum soil test category are based
on approximate nutrient removal for the harvested yield. The amounts shown
in the table for the optimum soil test category are based on 50 bu soybean grain per
acre. Nutrient removal amounts can be adjusted higher or lower for other yield levels.
Recommendations for soils with a corn suitability rating (CSR) of 30 or less should be based
on expected crop yield and nutrient removal for soil test categories of optimum
or lower.

Fine Textured
Sandy Textured

36–45
31–40

12–15

15–20

21–30
16–20

High

P2O5 to apply (lb/acre)
40
0

26–35
21–30

08–11

11–14

16–20
11–15

Optimum*

Potassium Soil Test (ppm)
Very Low

80

0–15
0–10

0–30

0–50

09–15
06–10

Low

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

Mehlich-3 ICP:
Low Subsoil P
High Subsoil P

High Subsoil P

Olsen P:
Low Subsoil P

Bray P1 and Mehlich-3 P:
Low Subsoil P
0–80
High Subsoil P
0–50

Soil Test Category:

Phosphorus Soil Test (ppm)

Table 4. Phosphorus and potassium recommendations for soybean
production.

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40

50

Very Low

Low

100

90

171–200
151–180

High

K2O to apply (lb/acre)
80
0

131–170
111–150

Optimum*

0

201+
181+

Very High

0

46+
41+

21+
16+

31+
21+

Very High

5  Iowa State University Extension
50

*The recommended amounts of P2O5 and K2O for the optimum soil test category are based
on approximate nutrient removal for the harvested yield. The amounts shown in the table
for the optimum soil test category are based on 80 bu oat grain per acre and straw. Nutrient
removal amounts can be adjusted higher or lower for other yield levels.

All Soil Textures

36–45
31–40

15–20
12–15

21–30
16–20

High

P2O5 to apply (lb/acre)
30
0

26–35
21–30

11–14
08–11

16–20
11–15

Optimum*

Potassium Soil Test (ppm)

16–25
11–20

0–15
0–10

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

Low Subsoil P
High Subsoil P

Mehlich-3 ICP:

06–10
04–70

0–50
0–30

Olsen P:
Low Subsoil P
High Subsoil P

Low
09–15
06–10

Very Low

Bray P1 and Mehlich-3 P:
Low Subsoil P
0–80
High Subsoil P
0–50

Soil Test Category:

Phosphorus Soil Test (ppm)

Table 5. Phosphorus and potassium recommendations for oat grain and
straw production.
Very Low

50

21–30

11–14

Low

70

40

171–200
151–180

High

K2O to apply (lb/acre)
15
0

131–170
111–150

Optimum*

0

201+
181+

Very High

0

51+

21+

31+

Very High

*The recommended amounts of P2O5 and K2O for the optimum soil test category are based
on approximate nutrient removal for the harvested yield. The amounts shown in the table
for the optimum soil test category are based on 50 bu wheat grain per acre. Nutrient removal amounts can be adjusted higher or lower for other yield levels.

All Soil Textures

41–50

18–20

26–30

High

P2O5 to apply (lb/acre)
30
0

31–40

15–17

21–25

Optimum*

Potassium Soil Test (ppm)
Very Low

60

0–20

0–10

16–20

Low

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

Mehlich-3 ICP:
All Subsoil P Levels

Olsen P:
All Subsoil P Levels

Bray P1 and Mehlich-3 P:
All Subsoil P Levels
0–15

Soil Test Category:

Phosphorus Soil Test (ppm)

Table 6. Phosphorus and potassium recommendations for wheat production.

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Very Low

Low

90

50

171–200
151–180

High

K2O to apply (lb/acre)
15
0

131–170
111–150

Optimum*

0

201+
181+

Very High

0

46+
41+

21+
16+

31+
21+

Very High

6  Iowa State University Extension
51

*The recommended amounts of P2O5 and K2O for the optimum soil test category are based
on approximate nutrient removal for the harvested yield. The amounts shown in the table
for the optimum soil test category are based on 2,000 lb sunflower seed per
acre. Nutrient removal amounts can be adjusted higher or lower for other yield levels.

All Soil Textures

36–45
31–40

15–20
12–15

21–30
16–20

High

P2O5 to apply (lb/acre)
15
0

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

50

70

26–35
21–30

11–14
08–11

16–20
11–15

Optimum*

Potassium Soil Test (ppm)

16–25
11–20

0–15
0–10

Mehlich-3 ICP:
Low Subsoil P
High Subsoil P

06–10
04–70

0–50
0–30

09–15
06–10

Low

Olsen P:
Low Subsoil P
High Subsoil P

Low Subsoil P
High Subsoil P

0–80
0–50

Very Low

Bray P1 and Mehlich-3 P:

Soil Test Category:

Phosphorus Soil Test (ppm)

Table 7. Phosphorus and potassium recommendations for sunflower
production.

90

16–25
11–20

06–10
04–70

09–15
06–10

Very Low

Low

240
220

210
200

171–200
151–180

High

K2O to apply (lb/acre)
175
0
175
0

131–170
111–150

Optimum*

0
0

201+
181+

Very High

0

46+
41+

21+
16+

31+
21+

Very High

*The recommended amounts of P2O5 and K2O for the optimum soil test category are based
on approximate nutrient removal for the harvested yield. The amounts shown in the table
for the optimum soil test category are based on approximately 22 tons corn silage per acre.
Nutrient removal amounts can be adjusted higher or lower for other
yield levels. At the high soil test category, banded NP or NPK starter fertilizer may be
advantageous under conditions of limited soil drainage, cool soil, crop residues on the soil
surface, or late planting dates with full-season hybrids. None is recommended for
the very high soil test category. Recommendations for soils with a corn suitability rating
(CSR) of 30 or less should be based on expected crop yield and nutrient removal for soil test
categories of optimum or lower.

Fine Textured
Sandy Textured

36–45
31–40

15–20
12–15

21–30
16–20

High

P2O5 to apply (lb/acre)
75
0

26–35
21–30

11–14
08–11

16–20
11–15

Optimum*

Potassium Soil Test (ppm)

105

0–15
0–10

0–50
0–30

0–80
0–50

Low

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

Mehlich-3 ICP:
Low Subsoil P
High Subsoil P

Olsen P:
Low Subsoil P
High Subsoil P

Low Subsoil P
High Subsoil P

Very Low

Bray P1 and Mehlich-3 P:

Soil Test Category:

Phosphorus Soil Test (ppm)

Table 8. Phosphorus and potassium recommendations for corn silage or sorghum silage production.

O-93

Low

280

171–200
151–180

High

K2O to apply (lb/acre)
240
200
0

131–170
111–150

Optimum*

Potassium Soil Test (ppm)

Very Low

41–50

18–20

26–30

High

0

201+
181+

7  Iowa State University Extension
52

Very High

0

51+

21+

31+

Very High

*For soils that test in the high soil test P category, 30 lb P2O5 per acre is recommended
at seeding time. The recommended amounts of P2O5 and K2O for the optimum soil test
category are based on 5 ton per acre of harvested hay. Nutrient removal amounts can be
adjusted higher or lower for other yield levels. For pastures, reduce the amount in all soil
test categories for phosphorus to two-thirds and for potassium to one-half of the amount
indicated for hay because more nutrients are returned to the soil when grazing.

All Soil Textures

31–40

15–17

21–25

Optimum*

P2O5 to apply (lb/acre)
80
60
0

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

0–20

Mehlich-3 ICP:
All Subsoil P Levels

110

11–14

0–10

Olsen P:
All Subsoil P Levels

21–30

16–20

Low

Bray P1 and Mehlich-3 P:
All Subsoil P Levels
0–15

Very Low

Very Low

Very Low

Low

180

140

171–200
151–180

High

K2O to apply (lb/acre)
100
0

131–170
111–150

Optimum*

0

201+
181+

Very High

0

46+
41+

16+

21+

31+
21+

Very High

*The recommended amounts of P2O5 and K2O in the optimum test category are based
on 3 ton per acre of harvested hay. Nutrient removal amounts can be adjusted higher or
lower for other yield levels. For pastures, reduce the amount in all soil test categories for
phosphorus to two-thirds and for potassium to one-half of the amount indicated for hay
because more nutrients are returned to the soil when grazing.

All Soil Textures

36–45
31–40

12–15

15–20

21–30
16–20

High

P2O5 to apply (lb/acre)
40
0

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

60

80

26–35
21–30

08–11

11–14

16–20
11–15

Optimum*

Potassium Soil Test (ppm)

16–25
11–20

4–70

6–10

9–15
6–10

Low

0–15
0–10

0–30

High Subsoil P
Mehlich-3 ICP:
Low Subsoil P
High Subsoil P

0–50

Olsen P:
Low Subsoil P

Bray P1 and Mehlich-3 P:
Low Subsoil P
0–80
High Subsoil P
0–50

Soil Test Category:

Phosphorus Soil Test (ppm)

Phosphorus Soil Test (ppm)

Soil Test Category:

Table 10. Phosphorus and potassium recommendations for clover- and trefoilgrass hay and pastures.

Table 9. Phosphorus and potassium recommendations for alfalfa and alfalfagrass hay and pastures.

O-94

Very Low

160

36–45
31–40

15–20
12–15

Low

120

171–200
151–180

High

K2O to apply (lb/acre)
80
0

131–170
111–150

Optimum*

0

201+
181+

Very High

0

46+
41+

21+
16+

31+
21+

Very High

8  Iowa State University Extension
53

*The amounts of P2O5 and K2O for the optimum category can be adjusted for approximate
nutrient removal for the harvested yield. For pastures, reduce the amount in all soil test categories for phosphorus to two-thirds and for potassium to one-half of the amount indicated
for hay because more nutrients are returned to the soil when grazing.

All Soil Textures

26–35
21–30

11–14
08–11

21–30
16–20

High

P2O5 to apply (lb/acre)
60
30
0

16–25
11–20

06–10
04–70

16–20
11–15

Optimum*

Potassium Soil Test (ppm)

Very Low

90

0–15
0–10

0–50
0–30

09–15
06–10

Low

Ammonium Acetate and Mehlich-3 Extractable K:
Low Subsoil K
0–90
91–130
High Subsoil K
0–70
71–110

Soil Test Category:

Low Subsoil P
High Subsoil P

Mehlich-3 ICP:

Low Subsoil P
High Subsoil P

Olsen P:

Bray P1 and Mehlich-3 P:
Low Subsoil P
0–80
High Subsoil P
0–50

Soil Test Category:

Phosphorus Soil Test (ppm)

Table 11. Phosphorus and potassium recommendations for tall cool-season
grasses, warm-season perennial grasses, and sorghum-sudan hay and
pastures.
Very Low

30

16–25

06–10

Low

All Soil Textures

40

30

36–45

15–20

21–30

High

171–200
K2O to apply (lb/acre)
0
0

131–170

Optimum

High

P2O5 to apply (lb/acre)
0
0

26–35

11–14

16–20

Optimum

Potassium Soil Test (ppm)
Very Low

40

0–15

0–50

09–15

Low

Ammonium Acetate and Mehlich-3 Extractable K:
All Subsoil K
0–90
91–130

Soil Test Category:

Mehlich-3 ICP:
All Subsoil P Levels

Olsen P:
All Subsoil P Levels

Bray P1 and Mehlich-3 P:
All Subsoil P Levels
0–80

Soil Test Category:

Phosphorus Soil Test (ppm)

0

201+

Very High

0

46+

21+

31+

Very High

Table 12. Phosphorus and potassium recommendations for bluegrass
dominant pasture.

O-95

0
0

0.5–0.8
Zn to apply broadcast (lb/acre)
5
Zn to apply in band (lb/acre)*
1

0–0.4
10
2

DTPA Extractable Zn:

9  Iowa State University Extension

Limestone recommendations (Table 14)
are given in pounds of pure fine calcium
carbonate (CaCO3). The recommended
amounts listed in Table 14 are for different soil Buffer pH, intended soil pH, and
depth of soil to be neutralized. Actual
rates of limestone to apply are calculated from the recommended CaCO3
rate (Table 14) and the effective calcium
carbonate equivalent (ECCE) of the
limestone product to be applied (ECCE
is determined for all agricultural limestone sources in Iowa). Soil pH is used

Limestone Recommendations

54

Recommendations are given to increase
soil pH to 6.5 or to 6.9. Soil pH 6.0 is
considered to be sufficient for grass pastures and grass haylands. Soil pH 6.9 is
recommended for alfalfa. Soil pH 6.5 is
considered to be sufficient for corn and

to determine whether or not to lime
the soil. The SMP Buffer (also termed
the Ohio Buffer) solution has been
calibrated to determine the amount of
lime required to increase soil pH to a
specific pH.

*Recommendation for amount to apply in band is based on other states’ information.

0.9+

Marginal

Low

Soil Test Category:

Zinc Soil Test (ppm)
Adequate

cy of occurrence of deficiencies with the
exception of iron deficiency on soybean.
Iron deficiency on soybean occurs on
high pH (calcareous) soils in central
and north central Iowa and can be
predicted by soil occurrence as shown
in soil survey reports. Development of
soybean varieties tolerant to low iron
availability in calcareous soils has been
an acceptable solution to the problem.

Table 13. Zinc recommendations for corn and sorghum production.

Soil test procedures for the other micronutrients have not been calibrated
because of either lack of or inconsisten-

Iowa State University recommends only
zinc (Zn) for corn and sorghum based
on soil testing. The Zn soil test has been
calibrated on Iowa soils. Zinc recommendations for corn and sorghum are
given in Table 13.

Micronutrients Recommendations
The amount of limestone recommended
is adjusted for the incorporation depth
from tillage, which determines the
volume of soil to be neutralized. The
equivalent depth for no-till is considered to be 2 to 3 inches.

3 inch
pH 6.5
pH 6.9

6 inch
pH 6.5
pH 6.9

8 inch
pH 6.5
pH 6.9

400
700
900
1,200
1,400
1,700
1,900
2,200
2,400
2,600
2,900

6.7
6.6
6.5
6.4
6.3
6.2
6.1
6.0
5.9
5.8
5.7

1,200
1,500
1,700
2,000
2,300
2,600
2,800
3,100
3,400
3,700
3,900

400
600
900

700
1,100
1,400
1,800
2,100
2,500
2,900
3,200
3,600
4,000
4,300

0
0
300

1,800
2,200
2,600
3,000
3,400
3,900
4,300
4,700
5,100
5,500
5,900

600
1,000
1,400

1,300
2,100
2,800
3,500
4,200
5,000
5,700
6,400
7,100
7,900
8,600

0
0
600

3,500
4,400
5,200
6,000
6,800
7,700
8,500
9,300
10,100
11,000
11,800

1,100
1,900
2,700

1,700
2,800
3,700
4,700
5,600
6,700
7,600
8,600
9,500
10,600
11,500

0
0
800

4,700
5,900
6,900
8,000
9,100
10,300
11,400
12,400
13,500
14,700
15,900

1,500
2,500
3,600

*Soil pH 6.9 is recommended for alfalfa. Soil pH 6.5 is considered to be sufficient for
corn and soybean. Because of high pH subsoils in the Clarion-Nicollet-Webster, GalvaPrimghar-Sac, Moody, Ida-Monona, Marshall, and Luton-Onawa-Salix soil associations, soil
pH 6.0 is considered sufficient for corn and soybean grown in these soil associations, but
when liming is required, lime to soil pH 6.5. Soil pH 6.0 is sufficient for grass pastures and
grass hayland.

0
0
200

- - - - - - - - - - - - - - - - - - - - - CaCO3 to apply (lb/acre) - - - - - - - - - - - - - - - - - - -

2 inch
pH 6.5
pH 6.9

7.0
6.9
6.8

Buffer
pH

Depth of soil to be neutralized*

Table 14. Lime recommendations, based on SMP Buffer Test, are given in
pounds of pure fine calcium carbonate (CaCO3) to increase soil pH from its
present level to pH 6.5 or 6.9 for the depth of soil to be neutralized.

soybean. Because of high pH (pH > 7.4)
in the subsoil of the Clarion-NicolletWebster, Galva-Primghar-Sac, Moody,
Ida-Monona, Marshall, and LutonOnawa-Salix soil associations, soil pH
6.0 is considered sufficient for corn and
soybean grown in these soil associations, but when liming is required, lime
is recommended to raise soil pH to 6.5.

O-96

10  Iowa State University Extension

54,144
7,871
9,223
47,346
6,090
10,234
24,260
5,430
22,927
545,763
6,276
40,208
9,480
27,685
1,174,150
5,967
6,140
6,560
19,125
14,940

19,679

Arenzville

Arenzville-Chaseburg Complex
Bertrand
Caneek
Chaseburg
Chelsea-Lamont-Fayette
Colo-Ely Complex
Dinsdale
Dockery
Dorchester
Downs
Downs Benches
Downs-Tama Complex
Eitzen
Exette
Fayette
Fayette Benches
Huntsville
Ion
Newvienna
Orion

Acres in Series

Soil Name

1. Loess-derived soils

H
H
H
H
L
H
L
H
H
H
H
H
L
H
H
H
H
L
H
H

H

Sub P

55

—continued

L
L
L
L
L
L
L
L
L
L
L
H
L
L
L
L
L
L
L
L

L

Sub K

A. Major soil area 1 that includes the Downs, Fayette, and Fayette-DubuqueStonyland soil associations.

Abbreviations used in the subsections of this table are as indicated:
Str Sub: stratified subsoil
R: rock
S&G: sand and gravel

Table 15. Subsoil phosphorus and potassium levels that are to be used
to determine phosphorus and potassium nutrient recommendations for
the major soil series in each of the 12 major soil areas in Iowa. Soil series
of more than 5,000 acres and with a corn suitability rating of 30 or greater
are listed. (Source: Iowa Soil Properties and Interpretations Database [ISPAID] 7.0,
revised November 2002)

Soils

5,878
14,374

H

L

Sub P

H
H
H
H
H
H

H
H
H

Sub P

L

L

Sub K

L
L
L
L
L
L

L
L
H

Sub K

35,020
48,635
7,238
11,540
51,420
9,754
12,735
7,722
6,405
30,630
7,094
15,046
207,339
250,218

Atterberry
Atterberry Benches
Atterberry Sandy Subsoil
Bassett
Bolan
Bremer
Calco
Chelsea-Lamont-Fayette
Colo
Colo-Ely Complex

Acres in Series

Ackmore
Ackmore-Colo Complex
Amana-Lawson-Perks
Ambraw

Soil Name

H
H
H
H
L
H
H
L
H
H

H
H
L
H

Sub P

—continued

L
L
L
L
L
H
L
L
L
L

L
L
L
L

Sub K

B. Major soil area 2 that includes the Dinsdale-Tama and Tama-Muscatine soil
associations.

Lamont

Jacwin

Soil Name

Acres in Series

24,968
14,800
23,880
15,710
19,150
11,167

Otter-Worthen Complex
Rozetta
Rozetta-Eleroy Complex
Sawmill
Tama
Worthen
2. Till-derived soils

27,947
6,250
6,180

Acres in Series

Orwood
Ossian
Otter Overwash

Soil Name

1. Loess-derived soils

A. Major soil area 1 that includes the Downs, Fayette, and Fayette-DubuqueStonyland soil associations, continued.

O-97

11  Iowa State University Extension

7,856
38,641
55,726
13,160
9,335
5,445
5,690
7,272
10,555
5,425
34,745
35,937

6,940
8,040
8,056
8,362
14,426
10,375
35,141
5,610
225,802

Klinger
Klinger-Maxfield Complex
Koszta
Lawler 32–40 To S&G
Lawson
Liscomb
Maxfield
Mt. Carroll
Muscatine

Muscatine Benches
Nevin
Nodaway
Nodaway-Arenzville Complex
Port Byron
Raddle
Radford
Richwood
Rowley
Saude
Sawmill
Sawmill-Garwin Complex

7,760
77,013
5,450
26,501
10,597
9,274
110,635

Fruitfield
Garwin
Garwin Sandy Subsoil
Judson
Kennebec
Kenyon
Killduff

L

H
H
H
H
H
H
H
H
H
L
H
L

L
L
H
L
H
L
L
H
H

L
L
L
H
H
L
H

H
H
H
L
H
H
H

56

—continued

L
H
L
L
L
L
L
L
L
L
L
L

H
L
L
L
L
L
L
L
L

L
L
L
H
H
L
L

L
L
L
L
L
L
L

L

5,122
26,515
5,225
22,137
8,535
24,783
16,691

14,510
11,590
16,005
841,398
18,759
23,777
8,895
24,465
H
H
H
H
H
H
H

H
H
L
H
H
H
L
H

L
L
L
L
L
H
L

L
L
L
L
L
L
L
L

377,687
24,697
5,095
38,379
52,688
8,070
8,984
16,760
7,790
51,687
43,369
47,455

16,568
8,405
5,205

Amana
Ambraw
Bremer
Clinton
Clinton Benches
Coland
Colo
Colo-Ely Complex
Colo-Zook Complex
Coppock
Ely
Fayette
Gara
Givin
Hedrick

Acres in Series

Soil Name

H
H
H
H
H
H
H
H
H
H
H
H

H
H
H

Sub P

—continued

L
L
L
L
L
L
L
H
L
L
L
L

L
L
H

Sub K

C. Major soil area 3 that includes the Otley-Mahaska-Taintor and Clinton-Keswick-Lindley soil associations.

Walford Benches
Waubeek
Waukee
Waukegan
Whittier
Wiota
Zook

Shaffton
Shelby
Sparta
Tama
Tama Benches
Tama Sandy Subsoil
Tama-Dickinson Complex
Walford

Sub K

13,545
358,010
70,560
16,560
20,551
34,295
5,000
20,145

Dinsdale
Downs
Downs Sandy Subsoil
Ely
Fayette
Fayette Sandy Subsoil
Franklin

Sub P

Dickinson

Acres in Series

Soil Name

Sub K

Acres in Series

Soil Name

Sub P

B. Major soil area 2 that includes the Dinsdale-Tama and Tama-Muscatine soil
associations, continued.

B. Major soil area 2 that includes the Dinsdale-Tama and Tama-Muscatine soil
associations, continued.

O-98

7,210
6,124
295,300
5,568
5,670
5,504
20,229
11,476
11,162
161,872
5,340
8,858
7,911
24,622

Nodaway-Vesser-Ackmore
Olmitz
Otley
Otley Benches
Otley-Nira Complex
Radford
Shelby
Sparta
Sperry

Taintor
Titus
Tuskeego
Vesser
Zook

12  Iowa State University Extension

281,324
14,194
6,175
44,305
212,911
5,200
75,880
39,128
15,373
13,318
9,725

11,675
23,015
16,095
5,588

Ladoga
Ladoga Benches
Lawson
Lindley
Mahaska
Nevin
Nira
Nodaway
Nodaway-Cantril Complex
Nodaway-Martinsburg Complex
Nodaway-Vesser Complex

Inton
Kalona
Keomah
Klum

L
H
H
H
H

L
L
H
H
H
H
L
L
H

H
H
H
H
H
H
H
H
L
H
H

H
L
H
L

L
L
L
L
L

L
H
L
L
L
L
L
L
H

L
L
L
L
H
H
L
L
L
L
L

H
L
L
L

57

Sub K

121,765
24,668
6,170
11,905
66,856
6,225
5,210
31,091
6,439
13,393
26,328
17,597

14,047
8,156
58,539
16,665
29,645
6,535
9,252
24,877
13,800
16,582
6,951
108,035
5,362
226,070
7,650
160,303

Caleb
Cantril
Cantril-Coppock-Nodaway
Chequest
Clarinda
Clearfield
Clearfield-Arispe Complex
Colo
Colo-Ely Complex
Coppock
Downs
Edina
Fayette
Gara
Gara-Armstrong Complex
Grundy
Haig
Humeston
Kennebec
Kennebec-Amana Complex
Kniffin
Ladoga
Ladoga Benches
Lamoni
Landes
Lawson
Lindley
Lineville

135,013
6,735
7,321
31,906

5,015
47,502
6,125
8,353

Arispe
Armstrong
Beckwith
Belinda

Ackmore
Adair
Amana
Appanoose

Acres in Series

H
H
H
H
H
H
H
L
L
H
H
L

L
L
L
H
L
H
L
H
H
H
H
L
H
H
L
H

L
L
H
H

H
L
H
H

Sub P

—continued

L
L
H
L
L
L
L
L
L
L
L
L

L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L

L
L
L
L

L
L
L
L

Sub K

Soil Name

Sub P

Soil Name

Acres in Series

D. Major soil area 4 that includes the Adair-Seymour, Grundy-Haig, Adair-Grundy-Haig, and Lindley-Keswick-Weller soil associations.

C. Major soil area 3 that includes the Otley-Mahaska-Taintor and Clinton-Keswick-Lindley soil associations, continued.

O-99

29,905
8,328
124,134
9,860
116,359
7,618
35,935
7,403
169,524
29,433
11,475

Pershing Benches
Rathbun
Seymour
Sharpsburg
Shelby
Tuskeego
Vesser
Wabash
Weller
Zook
Zook-Ely Complex

H
H
H
H
L
H
H
H
H
H
H

H
H
H
H
L
L
L
H

7,505
42,780
26,697
67,442
9,364
9,340
146,672
36,528

Clarinda
Clearfield
Clinton
Colo
Colo Overwash
Colo-Ackmore Complex
Colo-Ely Complex
Colo-Judson-Nodaway

13  Iowa State University Extension

9,380
30,255
10,931
6,206

Acres in Series

Ackmore
Adair Thin Solum
Adair-Shelby Complex
Bremer

Soil Name

L
H
H
H
H
H
H
H

H
L
L
H

Sub P

L
L
L
L
L
L
L
L

L
L
L
H

Sub K

L
L
L
H
L
L
L
H
L
L
L

H
L
L
L
L
H
L
L

58

—continued

E. Major soil area 5 that includes the Shelby-Sharpsburg-Macksburg soil
association.

8,385
19,600
36,717
14,038
12,710
20,020
203,026
218,817

Macksburg
Nira
Nodaway
Nodaway-Lawson-Ackmore
Nodaway-Lawson-Klum
Olmitz
Olmitz-Vesser-Colo
Pershing

Sub K

87,651
16,527
84,629
25,248
55,004
12,275
639,674
17,294
234,586
19,626
8,431
38,287
22,844
76,217
11,165

Sharpsburg Benches
Shelby
Tama
Vesser
Wabash
Winterset
Zook
Zook-Colo-Ely

11,697
59,582
5,400
14,752
8,808
160,886
30,780

14,100

Macksburg
Nevin
Nira
Nira-Sharpsburg Complex
Nodaway
Olmitz
Sharpsburg

Fayette
Gara
Humeston
Judson
Kennebec
Ladoga
Lamoni

Downs

Acres in Series

H
L
H
H
H
H
H
H

H
H
H
H
H
L
H

H
H
H
H
H
H
L

H

Sub P

Soil Name

Sub P

Soil Name

Acres in Series

E. Major soil area 5 that includes the Shelby-Sharpsburg-Macksburg soil
association, continued.

D. Major soil area 4 that includes the Adair-Seymour, Grundy-Haig, Adair-Grundy-Haig, and Lindley-Keswick-Weller soil associations, continued.

H
L
L
L
H
H
L
L

H
H
L
L
L
H
H

L
L
L
H
H
L
L

L

Sub K

O-100

6,420
926,427
44,816
6,673
50,630
53,090
5,515
98,318
34,400
55,426

Kennebec-Ackmore Complex
Marshall
Marshall Benches
Minden
Monona
Napier-Kennebec-Nodaway
Nevin
Nodaway
Shelby
Zook

H
H
H
H
L
L
H
H
L
H

H
H
H
H
L
H
H
L
H
H
H
L
L
H
L
L
L

L
L
L
H
H
H
H

L
H

14  Iowa State University Extension

Nodaway
Rawles

Calco
Castana
Ida
Kennebec
Kennebec-McPaul Complex
McPaul
McPaul-Kennebec Complex
Monona
Monona Benches
Napier

Soil Name

8,940
8,470

5,230
16,086
402,531
72,505
8,015
9,490
16,000
688,686
15,393
270,672

Acres in Series

H
H

H
L
L
H
H
H
H
H
H
L

Sub P

H
H

L
L
L
H
H
H
H
H
L
H

59

Sub K

G. Major soil area 7 that includes the Monona-Ida-Hamburg soil association.

6,994
69,125
473,474
7,226
234,720
118,471
62,245

Calco
Colo
Colo-Judson Complex
Ely
Exira
Judson
Kennebec

H
H

Woodbury

16,169

20,553
14,131
5,767
114,634
17,575
66,426
13,410
10,424
8,085
8,900
5,177
31,497
6,207
8,195
26,372
5,858

9,748
13,916
9,845
39,041

Cooper
Forney
Grable
Haynie
Keg
Lakeport
Lossing
Luton
Luton Thin Surface
McPaul
McPaul-Kennebec Complex
Modale
Moville
Napier-Castana Complex
Napier-Nodaway-Colo
Onawa
Owego
Percival
Salix
Tieville

16,117
7,267
5,920

54,983
20,158

Blencoe
Blend
Carr

Albaton
Blake

31,048
6,030

L

L
L
L
L
L
H
H
L
L
L
L
L
L
L
L
L

L
L
L
L

L
L
L

L
L

Sub P

Ackmore
Burchard

Acres in Series

Soil Name

Sub K

Acres in Series

Soil Name

Sub P

H. Major soil area 8 that includes the Luton-Onawa-Salix soil association.

F. Major soil area 6 that includes the Marshall soil association.

H

H
H
H
H
H
H
H
H
H
L
L
H
H
H
H
H

H
H
H
H

H
H
H

H
H

Sub K

O-101

15  Iowa State University Extension

11,195
7,960
5,561
9,280
17,241
5,910
23,815

5,445
159,279
24,494
13,358
366,779
59,045
12,555
169,598
7,195

Letri Calcareous
Marcus
Nicollet
Ocheyedan
Primghar
Radford
Ransom
Sac
Spicer

Spillco
Spillville
Steinauer
Terril
Tripoli
Wadena 24–32 To S&G
Wilmonton

59,439
1,068,182
67,332
15,715
9,005
7,255
26,265

Everly
Galva
Galva Benches
Galva Str Sub
Ida
Judson
Kennebec

H
L
L
L
L
L
L

L
L
L
L
L
H
L
L
L

L
L
L
L
L
H
H

H
H
H
H

L
L
L
L
L
L
L

L
L
L
H
L
L
L
L
L

L
L
L
L
L
H
H

L
L
L
H

60

97,943
28,610
5,970
7,235

5,700
17,620
153,555
5,015
13,100

L
L
L
L
L

Sub P

5,325
20,750
255,122

63,328
19,024
18,452
40,208
34,026
14,270
8,072
12,231
9,746
11,369
8,731
11,452
8,280

Coland-Spillville Complex
Collinwood
Colo
Crippin
Cylinder Deep
Cylinder Moderately Deep
Dickinson
Dickman
Estherville
Fieldon
Fostoria
Guckeen
Hanlon
Hanska
Harcot
Harps

16,208
56,321
57,027
10,371
1,297,749
1,629,066
26,815
83,342
134,671

43,703

Biscay Deep
Blue Earth
Bode
Brownton
Calco
Canisteo
Clarion
Clarion Long Slopes
Clarion-Storden Complex
Coland

Acres in Series

Soil Name

L
L
L

L
L
H
L
L
L
L
L
L
L
L
L
L

L
L
L
H
L
L
L
L
H

L

Sub P

K. Major soil area 11 that includes the Clarion-Nicollet-Webster soil
association.

Crofton
Egan
Moody
Moody Loamy Subsoil
Trent

Colo
Colo-Judson Complex
Davis
Ely

H
L
L
L
H

L
L
L
L
L

11,305
45,552
5,520
6,302
28,242

Ackmore
Afton
Allendorf
Bolan
Calco

Acres in Series

Soil Name

Sub K

Acres in Series

Soil Name

Sub P

J. Major soil area 10 that includes the Moody soil association.

I. Major soil area 9 that includes the Galva-Primghar-Sac soil association.

—continued

L
L
L

L
L
L
L
L
L
L
L
L
L
L
L
L

L
L
L
L
L
L
L
L
L

L

Sub K

L
L
L
L
L

Sub K

O-102

16  Iowa State University Extension

Terril
Truman Str Sub
Vinje
Wacousta
Wadena 24–32 To S&G
Wadena 32–40 To S&G
Waldorf
Webster
Webster-Nicollet Complex
Zenor

Linder
Luther
Marna
Mayer 24–32 To S&G
Mayer 32–40 To S&G
Nicollet
Okoboji
Okoboji-Harps Complex
Ottosen
Palms
Ridgeport
Rolfe
Spicer
Spillville
Storden
Talcot 32–40 To S&G

Kossuth
Le Sueur
Lester
Lester Long Slopes

29,781
7,020
6,836
20,232
77,175
31,082
24,575
918,520
77,907
15,938

8,683
8,684
23,015
6,662
5,620
1,067,487
318,210
40,776
72,172
35,517
16,714
5,355
5,882
66,514
109,067
45,340

76,968
14,598
104,111
5,050

L
H
L
L
L
L
L
L
L
H

L
H
L
L
L
L
L
L
L
H
H
L
L
H
L
L

L
H
H
H

L
H
H
L

L
L
L
L
L
L
L
L
L
L

L
L
L
L
L
L
L
L
L
L
H
H
L
L
L
L

L
L
L
L

L
L
L
L

61

Hayfield 24–40 To S&G
Hoopeston
Jameston
Kenyon
Klinger
Lamont
Lawler 24–32 To S&G
Lawler 32–40 To S&G
Lourdes

Clyde
Clyde-Floyd Complex
Coggon
Coland
Cresco
Dickinson
Dickinson Loamy Subsoil
Dickinson-Ostrander Complex
Dinsdale
Donnan
Downs
Finchford
Flagler
Floyd
Franklin
Hayfield 24–32 To S&G

Bassett
Bolan
Burkhardt-Saude Complex
Chelsea

Ansgar
Aredale
Ashdale
Atkinson

9,739
7,317
6,484
591,170
139,349
7,542
37,772
50,196
19,330

381,543
318,086
7,078
25,785
47,728
84,505
15,850
5,039
44,033
24,633
9,558
10,170
42,799
256,708
23,132
23,484

140,498
26,491
6,857
12,351

9,495
37,724
6,255
6,978

H
L
L
L
L
H
L
L
L

L
L
H
H
L
L
L
L
H
L
H
H
L
L
H
H

H
L
L
L

H
L
H
L

L
L
L
L
H
L
L
L
L

L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L

L
L
L
L

L
L
L
L

Sub K

—continued

13,735
37,778
13,704
24,276

Sub P

Havelock
Hayden
Kilkenny
Knoke

Acres in Series

Soil Name

Sub K

Acres in Series

Soil Name

Sub P

L. Major soil area 12 that includes the Kenyon-Floyd-Clyde and CrescoLourdes-Clyde soil associations.

K. Major soil area 11 that includes the Clarion-Nicollet-Webster soil
association, continued.

O-103

17  Iowa State University Extension

Marshan 24–32 To S&G
Marshan 32–40 To S&G
Maxfield
Olin
Oran
Ostrander
Palms
Protivin
Racine
Readlyn
Riceville
Rockton 20–30 To R
Rockton 30–40 To R
Rossfield
Sattre
Saude
Schley
Seaton
Sparta
Spillville
Spillville-Coland Complex
Tama
Terril
Tripoli
Turlin
Udolpho
Wapsie
Waubeek
Waukee
Winneshiek

Soil Name
27,264
88,781
63,479
63,200
83,395
94,518
10,864
34,767
43,776
200,316
13,283
38,953
22,146
8,075
6,566
133,715
61,513
6,008
70,253
34,753
29,291
5,850
22,225
102,559
5,218
5,105
52,150
9,387
61,392
25,549

Acres in Series
L
L
L
L
L
L
L
L
L
L
L
L
L
H
H
L
L
H
L
L
L
H
L
L
L
H
H
H
H
H

Sub P

L. Major soil area 12 that includes the Kenyon-Floyd-Clyde and CrescoLourdes-Clyde soil associations, continued.

L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L

62

Sub K

O-104

9

GPS

Sioux

Lyon

Hamilton

Wright

Hancock

Hardin

Franklin

Cerro
Gordo

Worth

Shelby

Harrison

5

Cass

Taylor

Adams

SSM

Adair

Dallas

Ringgold

AGH

4
Lucas

West East

Wayne

LKW

Monroe

Appanoose

Marion

Tama

Mahaska

TM
Jasper

LKW

Warren

Decatur

Clarke

Story

Polk

CKL

Boone

Madison

Union

Greene

Guthrie

Carroll

Audubon

Montgomery

Fremont Page

Mills

Pottawattamie

M

6

7

Crawford

Iowa

ASE

Davis

GH

Wapello

4

1

F

Van
Buren

LKW

Jefferson

CKL

Lee

3

Henry

OMT

Washington

OMT

2

Muscatine

4

Des B
Moines

3

B

2
F
1

2

F

Clinton

KFC

TM 2

F

TM Scott

Cedar

Louisa

TM

DT

Jones

1

Jackson

FDS
Dubuque

FDS

Delaware

1

Clayton

Johnson
CKL

2

Linn

Buchanan

12

Fayette

F

D

F

Winneshiek Allamakee

Benton

Keokuk

3

F

Black
Hawk

Bremer

Poweshiek

Grundy

DT

Chickasaw

CLC

Howard

KFC
Butler

Floyd

Mitchell

1

12

Adair-Grundy-Haig
Adair-Seymour-Edina
Clinton-Keswick-Lindley
Cresco-Lourdes-Clyde
Clarion-Nicollet-Webster

18  Iowa State University Extension

AGH:
ASE:
CKL:
CLC:
CNW:
D:
DT:
F:
FDS:
GPS:

Downs
Dinsdale-Tama
Fayette
Fayette-Dubuque-Stonyland
Galva-Primghar-Sac

63

GH:
KFC:
LKW:
LOS:
M:

Grundy-Haig
Kenyon-Floyd-Clyde
Lindley-Keswick-Weller
Luton-Onawa-Salix
Marshall

MIH:
Mo:
OMT:
SSM:
TM:

Monona-Ida-Hamburg
Moody
Otley-Mahaska-Taintor
Shelby-Sharpsburg-Macksburg
Tama-Muscatine

Figure 1. Map of Iowa delineating the 21 principal soil association areas (letters) and the 12 major soil areas (numbers). B designates the Mississippi
bottomland.

8

Webster

11

Humboldt

CNW

Kossuth

Winnebago

Marshall

Calhoun

Pocahontas

Palo
Alto

Emmet

Monona

Sac

Buena
Vista

Clay

Dickinson

2

Ida

Cherokee

O’Brien

Osceola

MIH

Woodbury

Plymouth

LOS

10

MO�

West East

O-105

64

Prepared by J. E. Sawyer, A. P. Mallarino,
R. Killorn, and S. K. Barnhart, Department of Agronomy, Iowa State University.

File: Agronomy 8-2

Issued in furtherance of Cooperative
Extension work, Acts of May 8 and
June 30, 1914, in cooperation with
the U.S. Department of Agriculture. Jack
M. Payne, director, Cooperative Extension Service, Iowa State University of
Science and Technology, Ames, Iowa.

Crop Nutrient and Limestone Recommendations in Iowa  19

. . . and justice for all
The U.S. Department of Agriculture
(USDA) prohibits discrimination in all
its programs and activities on the basis
of race, color, national origin, gender,
religion, age, disability, political beliefs,
sexual orientation, and marital or family
status. (Not all prohibited bases apply
to all programs.) Many materials can be
made available in alternative formats for
ADA clients. To file a complaint of discrimination, write USDA, Office of Civil
Rights, Room 326-W, Whitten Building,
14th and Independence Avenue SW,
Washington, DC 20250-9410 or call
202-720-5964.

O-106

O-107

Using Manure Nutrients
for Crop Production
Nutrients in Animal Manure
Manure can supply nutrients required
by crops and replenish nutrients
removed from soil by crop harvest.
Since manure contains multiple
nutrients, applications should
consider not only what is needed
for the crop to be grown but also
how the ratio of nutrients in manure
could affect soil test levels. This
ensures adequate nutrient supply
and reduces potential for over- or
under-application and subsequent
buildup or depletion in the soil.
Good manure nutrient management
should consider short-term and longterm impacts on crop nutrient supply
and soil resources.

Manure has characteristics that make
nutrient management different and
sometimes more complicated than
fertilizer. These include a mix of
organic and inorganic nutrient forms;
variation in nutrient concentration
and forms; variation in dry matter
and resultant handling as a liquid
or solid; and relatively low nutrient
concentration requiring large application volumes. Since manure nutrient
composition can vary significantly,
sampling and laboratory analysis are
always needed, while with fertilizer
nutrient concentrations are provided
at a guaranteed analysis.

The manure nutrient concentration
varies considerably between animal
species; dietary options; animal genetics; animal performance; production
management and facility type; and
collection, bedding, storage, handling,
and agitation for land application.
Use of average or “book” nutrient
values can be helpful for designing
a new facility and creating manure
management plans but is not very
helpful in determining specific
manure nutrient supply or application rates due to wide variation in
nutrient concentrations between
production facilities. For example, a
recent sampling across swine finishing
facilities found a range in total N from
32 to 79 lb N/1,000 gal, P from 17 to
54 lb P2O5 /1,000 gal, and K from 23
to 48 lb K2O/1,000 gal. A similar or
larger range can be found with other
manure types. Nutrient analyses often
vary greatly as storage facilities are
emptied or manure is stockpiled, and
also among multiple samples collected
from loads during land application.
Therefore, collecting multiple manure
samples and maintaining a history
of analysis results will improve use
of manure nutrients.
For determining manure application
rates and equating to crop fertilization
requirements, it is most helpful if
manure analyses give N, P2O5, and
K2O based on an as-received or wet
basis in lb per ton or lb per 1,000 gal
units. It is beyond the scope of this
publication to give detailed manure
sampling and laboratory analysis

PMR 1003 September 2008

65

O-108
Using Manure Nutrients for Crop Production
recommendations. Those can
be found in the extension materials
listed on page 7. If manure analyses
are provided from the laboratory in
other units, they must be converted
to these units. See the ISU Extension
manure sampling publication for
appropriate conversion factors. If
manure average nutrient values or
methods to estimate manure nutrient
concentrations based on excretion
are of interest or needed for planning
purposes, those can be found in the
Midwest Plan Service bulletins listed
on page 7.

Manure Nutrient Availability
for Crops
Nutrient management guidelines
use the words “manure nutrient
availability” when suggesting manure
applications to supply nutrients
needed by crops. However, the
meaning of “availability” for manure
nutrients often is not clear or its use
not consistent. Available is defined as
present or ready for immediate use, or
present in such chemical or physical
form as to be usable (as by a plant).
The main reasoning for using
the term “available” in describing
manure nutrients is that some
portions are in forms that cannot
be used by plants immediately upon
application to soil and have to be
converted to a form that plants can
take up. The term “available” is not
typically applied to fertilizers because
most include chemical forms that
plants can take up or are quickly
converted upon application to soil.
According to this definition, most
inorganic fertilizers contain basically

2

100 percent crop-available nutrients.
For example, anhydrous ammonia
dissolves in water and rapidly changes
to ammonium, urea hydrolyzes to
ammonium within a few days, and
ammonium is further transformed to
nitrate by soil microorganisms. Monoammonium phosphate (MAP) and
diammonium phosphate (DAP) are
highly soluble in water and dissolve
to ammonium and orthophosphate.
Potassium chloride (KCl, potash),
dissolves in water to potassium
(K+) and chloride (Cl–) ions. Both
orthophosphate and K ions are taken
up by plants. Because all K contained
in manure is in the K+ ionic form,
manure K is readily crop available in
all manure sources.
For manure N and P, there is usually
a mix of organic and inorganic
materials that varies among manure

66

sources, production systems, bedding,
storage, and handling. This variety
in forms of N and P in manure
contributes to greater uncertainty in
manure nutrient management compared with fertilizers. The ratio of
inorganic (mainly ammonium) and
organic N varies considerably with
the manure source. This was shown,
for example, by on-farm research that
included manure sampling and analysis from swine and poultry operations.
The fraction of total N as ammonium
N was almost 100 percent for swine
manure from the liquid portion of
anaerobic lagoons, 65 to 100 percent
(average 84 percent) for liquid swine
manure from under-building pits or
storage tanks, and 10 to 40 percent
(average 20 percent) for solid poultry
manure. The large ammonium-N
concentration and organic-N fraction
that is easily mineralized after applica-

O-109
Using Manure Nutrients for Crop Production
tion to soil explain why N in liquid
swine manure is considered “highly”
crop available and almost comparable
to fertilizer N. Other manures have
lower ammonium-N concentrations
and greater (and tougher to degrade)
organic materials due to bedding
and feed materials. Considerable P
in swine manure is orthophosphate
and calcium phosphate compounds
(derived both from feed and mineral
supplements added to rations) that
are soluble or dissolve quickly once
applied to soil. The rest is organic P,
which varies greatly in complexity
and reaction in soil. Testing manure
for ammonium-N or water-soluble
N can be a way of estimating immediately available N. Unfortunately, a
similarly useful test does not exist for
P. Therefore, the availability estimate
for manure N and P can be, and often
is, less than 100 percent of total N
and P.

Manure Nutrient Supply
There is a clear difference between
crop availability of nutrients in
fertilizer or manure and seasonlong supply of nutrients. Significant
amounts of plant usable forms of
nutrients in both fertilizer and manure
might be lost and became unavailable
to crops after application. For example, N can be lost through processes
such as leaching, volatilization, or
denitrification while P can be lost
through erosion and surface runoff.
Also, these nutrients can be converted
for short or long periods of time into
forms not usable by plants through
processes such as immobilization
to organic materials for N and

retention by soil mineral constituents
for P. Nutrient loss issues are not as
pertinent for P and K as for N in
Iowa soils as long as there is little
soil erosion and surface runoff.
The immediate or long-term fate of
plant usable nutrients in soil can
be similar for manure and fertilizer.
However, variation in manure
nutrient concentration, application
rate, and application distribution
affect nutrient supply and contribute
to increased uncertainty with manure
management. Application rate and
distribution uncertainties affect all
applied nutrient sources but are more
difficult to manage with manure than
with fertilizer. With careful manure
sampling, pre-application nutrient
analysis, study of nutrient analysis
history, and calibration of application
equipment, reasonable manure
nutrient application rates can be
achieved. Due to material characteristics, and sampling and analysis
variability, field distribution and
application rate variability often is
greater for dry manure sources.
These supply issues can be important
for N, P, and K, although typically are
of greater concern with N. There are
several reasons, including manure
usually is applied for corn production where N supply is critical, many
Iowa soils have optimum or higher P
and K test levels where need for and
response to P and K is much less than
with N, and crop deficiency symptoms
and yield loss resulting from nutrient
supply problems are more obvious
for N.

67

Manure nutrient loss, application
rate, and distribution uncertainties
usually are not included in crop nutrient availability estimates. Instead, they
are handled by suggested management
practices. Not all published guidelines are consistent in this regard and,
therefore, suggested crop nutrient
availabilities do vary between states
and regions. In this publication, use
of “availability” refers to manure
nutrients potentially available for
plant uptake (with no losses) by the
first crop after application or beyond,
and percent nutrient availability
values provided correlate to those for
commonly used fertilizers. The guidelines in this publication assume supply issues are handled in the best way
possible as is done with fertilizers.
It is important to understand that for
successful manure nutrient management, in many instances supply issues
are as, or more, critical than estimates
of nutrient availability.
Improving crop nutrient supply with
manure can be achieved by understanding the issues related to manure
nutrient analysis, application rate,
application distribution, and the
benefits and risks related to management practices such as application
timing and placement that influence
potential losses. Additionally, use of
available tools to determine initial soil
nutrient levels and adjust application
rates can help provide for adequate
season-long nutrient supply when
either manure or fertilizer is used.
These tools include commonly used
pre-plant soil testing for P and K,
estimates of N application rate need
based on response trial data (such as

3

O-110
Using Manure Nutrients for Crop Production
the Corn Nitrogen Rate Calculator),
and tools to help determine need for
additional N after planting corn such
as the late-spring soil nitrate test and
in-season crop sensing for N stress.

Manure Nutrient Application
Recommendations
To determine manure application
rates, the following information is required: needed crop nutrient fertilization rate for N, P, K, or other deficient
nutrients; manure type; nutrient
analysis; nutrient crop availability;
and method of application. Nutrient
recommendations for crops are provided in other Iowa State University
Extension publications and are not
repeated here (see list on page 7).

Once the needed nutrient application
rate is determined, the manure rate
to supply crop available nutrients
is calculated based on the specific
manure source being used.
An additional consideration is what
portion of the needed fertilization will
be supplied from manure—to meet
the full crop nutrient requirement, or
a partial requirement from manure
and the remaining from fertilizer. This
is an important consideration because
manure contains multiple nutrients
and a manure rate to supply the most
deficient nutrient can over-supply
other nutrients. Also, manure application to meet the least deficient or most
environmentally restrictive nutrient
application can result in under-supply
of other nutrients.

In these cases, use of fertilizers in
addition to manure application is
necessary to appropriately meet all
nutrient application requirements.

Manure Nutrient
Availability Values
Many of the manure N, P, and K
crop availability estimates listed in
Table 1 are derived from research
trials conducted in Iowa. However,
when local research is lacking,
applicable information was taken
from research conducted in other
states. For manure sources not listed
in the table, values based on manure
with similar characteristics can
provide a reasonable estimate.

First-Year Availability Estimates
Table 1. First-year nutrient availability for different animal manure sources.
Manure Source

Nitrogen1

Phosphorus2

Potassium2

- - - - - - - - - - - - - - Percent of Total Nutrient Applied - - - - - - - - - - - - - Beef cattle (solid or liquid)

30–40

60–100

90–100

Dairy (solid or liquid)

30–40

60–100

90–100

Liquid swine (anaerobic pit)

90–100

90–100

90–100

Liquid swine (anaerobic lagoon)

90–1003

90–1003

90–100

Poultry (all species)

50–60

90–100

90–100

1

The estimates for N availability do not account for potential volatile N losses during and after land application. Correction factors for volatile
loss are given in Table 2. The ranges are provided to account for variation in the proportion of ammonium N (and for poultry manure also uric
acid), bedding type and amount, and both sampling and analysis.
2
The ranges in P and K availability are provided to account for variation in sampling and analysis, and for needed P and K supply with different
soil test levels. A small portion of manure P may not be available immediately after application, but all P is potentially available over time.
Use lower P and K availability values for soils testing in the Very Low and Low soil test interpretation categories, where large yield loss could
occur if insufficient P or K is applied and a reasonable buildup is desirable. Use 100% when manure is applied to maintain soil-test P and K in
the Optimum soil test category, when the probability of a yield response is small.
3

Values apply for the liquid portion of swine manure in lagoons; the N and P availability will be less and difficult to estimate with settled solids.

4

68

O-111
Using Manure Nutrients for Crop Production
Second- and Third-Year Availability Estimates
While manure N may become crop
available over multiple years for
some sources, there should not
be an expectation that all of the
manure N will eventually become
crop available. This happens
because some of the N is in
difficult to degrade organic forms
(recalcitrant) and will become part
of the soil organic matter. For
some manure sources, such as
with bedded systems, not all of the
manure N should be accounted
for in manure plans over multiple
years and the first-, second-, or
third-year availability may not add
up to 100 percent.
Animal manure that has considerable organic material can have
some residual-N availability in
the second or third year after
application. The second-year N
availability estimate for beef cattle
and dairy manure is 10 percent,

and 5 percent for the third year.
Other manures that have similar
organic N and bedding could have
similar second- and third-year N
availability. Manure sources that
have low organic N will not have
second-year crop available N. These
include liquid systems like swine
manure stored in under-building
pits and above-ground tanks, and
anaerobic lagoons. Poultry manure,
since it has considerable organic
material, has some but low secondyear (0–10 percent) availability
and no third-year N availability.
The P and K contained in
animal manure are estimated at
100 percent crop available over a
long term. Residual effects of P and
K not used in the year of application will be reflected in soil tests
and crop use, just like fertilizer P
and K applied for one year or for
multiple years.

69

Adjusting for Manure
Nitrogen Volatilization
The estimates for manure N availability in Table 1 do not consider
potential volatile N losses during
or after application. Losses are from
various volatile N compounds in
manure, such as ammonia, and
ammonia that is produced when
urea, uric acid, or other compounds
convert to ammonium. These are
similar losses that can occur from
some N fertilizers such as anhydrous
ammonia, urea, and urea-ammonium
nitrate (UAN) solutions. If manure
is left on the soil surface, losses may
occur until N is moved into the soil
with rainfall or incorporated with
tillage. Many factors affect the rate
and amount of volatile loss, such as
temperature, humidity, rainfall, soil
moisture, soil pH, surface residue
cover, and days to incorporation.
Volatile losses at or after application
often are difficult to predict accurately.
However, losses can be significant,
and, therefore, it is important to make
an adjustment for volatile N losses
from applied manure and for manure
management planning purposes.
Values given in Table 2 provide
guidance on potential volatile
losses. The correction factors in
Table 2 do not account for N losses
during storage and handling (time
from excretion to sampling for
analysis) and assume a reasonable
time period from sampling to land
application so that the manure
analysis represents the manure
being applied. To estimate manure
N remaining in soil after application,
multiply the applied manure N rate
by the appropriate correction factor.

5

O-112
Using Manure Nutrients for Crop Production
Table 2. Correction factors to account for N volatilization losses during and after land application of animal
manure.1
Incorporation

Volatilization Correction Factor2

—

0.98–1.00

Immediate incorporation

0.95–0.99

Broadcast (liquid)

No incorporation

0.75–0.90

Broadcast (solid)

No incorporation

0.70–0.85

Irrigation

No incorporation

0.60–0.75

Application Method
Direct injection
Broadcast (liquid/solid)

1

Adapted from Midwest Plan Service MWPS-18, Third Edition. Nitrogen losses during and within four days of application.

2

Multiply the manure total N rate applied times the volatilization correction factor to determine the portion of total manure N remaining.

Considerations for Time
of Application
The time of application influences
nutrient availability and potential
manure and nutrient loss from soil.
Fall applications allow more time
for organic N and P portions of
manure to mineralize so they are
available for plant uptake the next
crop season. This is more important
for N in manures with high organic
matter content, such as bedded
systems. Iowa research has shown
that fall versus springtime P and
K application usually is not an
agronomic issue for fertilizers or
manure. The increased time for
organic N mineralization with fall
application also allows for nitrification

6

of ammonium and therefore more
potential nitrate loss through leaching or denitrification with excessively
wet spring conditions. This is a more
important issue for manure with large
ammonium-N concentration, such as
liquid swine manure. Coarse-textured
soils, with high permeability, are the
most likely to have leaching losses.
Fine- and moderately fine-textured
soils, prone to excess wetness, are
most likely to have denitrification
losses. Manure applied in the spring
has less time for organic N and P
mineralization before crop uptake.
Delayed mineralization can be an
important issue for manure with high
organic matter content, especially
in cold springs. With manure that

70

contains a large portion of N as
ammonium, spring application
allows for better timing of nitrification
to nitrate and subsequent crop use,
and less chance of N loss.
As a general rule, do not apply
manure in the fall unless the soil
temperature is 50° F and cooling at
the four-inch soil depth. This will
slow the mineralization and nitrification processes and is an especially
important consideration for manure
containing a large portion of N
as ammonium.
Broadcasting manure onto frozen,
snow-covered, water-saturated soils
increases the potential for nutrient
losses with rainfall or snowmelt
runoff to surface water systems.
If manure must be applied in these
conditions, it should be applied on
relatively flat land, slopes less than
5 percent, and well away from
streams and waterways (see Iowa
Department of Natural Resources
rules on setback distances).

O-113
Using Manure Nutrients for Crop Production
Example Calculation of Manure Application Rates

Additional Resources

Note: The N, P, and K fertilization requirements in these examples are
determined from appropriate extension publications and Web-based tools listed
at the right.

PM 1688 A General Guide for
Crop Nutrient and Limestone
Recommendations in Iowa

Example 1

Example 2

b Manure source: liquid swine manure,
finishing under-building pit.

b Manure source: solid layer manure.

b Manure analysis: 40 lb N/1,000 gal, 25 lb
P2O5/1,000 gal, 35 lb K2O/1,000 gal.
b Intended crop: corn in a corn-soybean
rotation.
b Soil tests: 19 ppm Bray P-1 (Optimum),
165 ppm Ammonium Acetate K
(Optimum).
b Crop yield and P and K removal for
determining nutrient rates needed to
maintain the Optimum soil test category:
200 bu/acre corn yield; 75 lb P2O5/acre
and 60 lb K2O removal.
b Manure rate: based on corn N fertilization
requirement at 125 lb N/acre.
b Manure application: injected late fall.
b Manure nutrient availability: 100 percent
for N, P, and K.
b Manure N volatilization correction factor:
0.98.
b Manure rate: 125 lb N/acre ÷ (40 lb N/
1,000 gal 3 0.98) = 3,200 gal/acre.
b Manure available P and K nutrients
applied: 3,200 gal/acre 3 (25 lb P2O5/
1,000 gal 3 1.00) = 80 lb P2O5/acre; and
3,200 gal/acre 3 (35 lb K2O/1,000 gal 3
1.00) = 112 lb K2O/acre.
b Phosphorus and K applied with the
manure are adequate for P (slightly more
than expected corn removal) and will
supply more than needed K. The extra
P and K can be used by the next crop
and should be accounted for. However,
additional P and K will need to be applied
for the following soybean crop.

b Manure analysis: 72 lb N/ton, 69 lb
P2O5/ton, 54 lb K2O/ton.
b Intended crop: corn-soybean rotation.
b Soil tests: 18 ppm Bray P-1 (Optimum),
120 ppm Ammonium Acetate K (Low).
b Manure rate: based on P requirement for
the crop rotation at 120 lb P2O5/acre.
b Manure application: late fall, incorporated
after four days.
b Manure nutrient availability: 55 percent
for N, 100 percent for P and K.
b Manure N volatilization correction factor:
0.80.
b Manure rate: 120 lb P2O5/acre ÷ (69 lb
P2O5/ton 3 1.00) = 1.7 ton/acre.
b Manure available N and K nutrients
applied: 1.7 ton/acre 3 (72 lb N/ton 3
0.60 3 0.80) = 60 lb N/acre; and
1.7 ton/acre 3 (54 lb K2O/ton 3 1.00)
= 92 lb K2O/acre.
b Corn N fertilization need and K needed
for the corn and soybean crops with a
Low soil test category: 130 lb N/acre and
172 lb K2O/acre.
b Crop available N and K applied with
manure is not adequate for N, need
additional 70 lb fertilizer N/acre (130 lb
N/acre – 60 lb N/acre); and applied K is
not adequate for the corn and soybean
crops, need additional 80 lb K2O/acre
(172 – 92 lb K2O/acre) from fertilizer.

71

PM 287 Take a Good Sample to Help
Make Good Decisions
PM 2015 Concepts and Rationale
for Regional Nitrogen Rate Guidelines
for Corn
PM 1714 Nitrogen Fertilizer
Recommendations for Corn in Iowa
PM 2026 Sensing Nitrogen Stress
in Corn
PM 1584 Cornstalk Testing to Evaluate
Nitrogen Management
PM 1588 How to Sample Manure
for Nutrient Analysis
A3769 Recommended Methods of
Manure Analysis (University of
Wisconsin)
MWPS-18-S1 Manure Characteristics:
Section 1 (Midwest Plan Service)
MWPS-18 Livestock Waste Facilities
Handbook, Third Edition (Midwest
Plan Service)
Corn Nitrogen Rate Calculator,
http://extension.agron.iastate.edu/
soilfertility/nrate.aspx

7

O-114
Using Manure Nutrients for Crop Production
Summary
b

Carefully manage the nutrients
in animal manure as you would
manage fertilizer.

b

Have representative manure samples
analyzed to determine nutrient
concentration. At a minimum,
samples should be analyzed for
moisture (dry matter) and total N,
P, and K. For additional information
on N composition, samples can be
analyzed for ammonium. Maintain
a manure analysis history for
production facilities.

b

b

Set the manure application rate
according to crop fertilization
requirements and for the crop
availability of manure N, P, and K.
Adjust manure rates for estimated
N volatilization.

8

b

b

For manure application rates,
consider the crop N, P, and K
fertilization requirements and field
P-Index ratings, but do not exceed
the crop N fertilization need.
Consider the nutrient needs of crop
rotations rather than just individual
crops, which is especially important
for P and K management.

b

Allocate manure to fields based on
soil tests and crops to be grown.

b

Fall applications of manure should
not be made until the soil temperature is 50° F and cooling, especially
for manure sources that have a large
portion of N as ammonium.

b

Do not apply manure to snowcovered, frozen, or water-saturated
sloping ground to reduce risk of
nutrient loss and water quality
impairment.

72

Prepared by John E. Sawyer and Antonio P.
Mallarino, professors of agronomy and
extension soil fertility specialists,
Iowa State University.
This publication was peerreviewed by three independent
reviewers using a double-blind process.

. . . and justice for all
The U.S. Department of Agriculture (USDA)
prohibits discrimination in all its programs and
activities on the basis of race, color, national
origin, gender, religion, age, disability, political
beliefs, sexual orientation, and marital or family
status. (Not all prohibited bases apply to
all programs.) Many materials can be made
available in alternative formats for ADA clients.
To file a complaint of discrimination, write USDA,
Office of Civil Rights, Room 326-W, Whitten
Building, 14th and Independence Avenue, SW,
Washington, DC 20250-9410 or call 202-720-5964.
Issued in furtherance of Cooperative Extension
work, Acts of May 8 and June 30, 1914, in
cooperation with the U.S. Department of
Agriculture. Jack M. Payne, director, Cooperative
Extension Service, Iowa State University of Science
and Technology, Ames, Iowa.

How to Sample Manure
for Nutrient Analysis

O-115

A field-by-field nutrient management program requires multiple components to maintain adequate fertility
for crop growth and development. A well-designed soil sampling plan, including proper soil test interpretations along with manure sampling, manure nutrient analysis, equipment calibration, appropriate application
rates and application methods are all necessary components of a nutrient management plan. Implementing
these components allows manure to be recognized and used as a credible nutrient resource, potentially
reducing input costs and the potential of environmental impacts.
Animal manure has long been used as a source of nutrients for crop growth. Standard nutrient values are
guides to determine the amount of nutrients that animal manure will supply as a fertilizer source. Iowa State
University Extension publication, Managing Manure Nutrients for Crop Production (PM 1811), recommends
manure nutrient content and credits by type of animal, handling system and application methods.
While “book values” like those in PM-1811 are reasonable average values, an individual farm’s manure
analyses can vary from those averages by 50 percent or more. Species, age of animal, feed rations, water use,
bedding type, management, and other factors make every farm’s manure different. Two key factors affecting
the nutrient content of manure are manure handling and type of storage structures used. Each handling
system results in different types of nutrient losses—some unavoidable and others that can be controlled to a
certain degree. Because every livestock production and manure management system is unique, the best way
to assess manure nutrients is by sampling and analyzing the manure at a laboratory.
This publication describes how to sample solid, semi-solid, and liquid manure. Manure with greater than 20
percent solids (by weight) is classified as dry manure and is handled as a solid, usually with box-type spreaders. Manure with 10 to 20 percent solids is classified as semi-solid manure and can usually be handled as a
liquid. Semi-solid manure usually requires the use of chopper pumps to provide thorough agitation before
pumping. Manure with less than 10 percent solids is classified as liquid manure and is handled with pumps,
pipes, tank wagons, and irrigation equipment.
A representative manure sample is needed to provide an accurate reflection of the nutrient content. Unfortunately, manure nutrient content is not uniform within storage structures, so obtaining a representative sample
can be challenging. Mixing and sampling strategies should therefore insure that samples simulate as closely
as possible the type of manure that will be applied.

When to Sample Manure
Sampling manure prior to application will ensure that you receive the analysis in time to adjust
nutrient application rates based on the nutrient concentration of the manure. However, sampling manure prior to application may not completely reflect the nutrient concentration of the
manure due to storage and handling losses if long periods of time pass before application begins
or when liquid storage facilities are not adequately agitated while sampling. “Pre-sampling”
such as dipping samples off the top of storage structure for nitrogen (N) and potassium (K)
concentrations, can be done to estimate application rates. (See page 3 for more on pre-sampling). Producers must remember to go back and determine the actual nutrient rates applied by
using manure samples collected during application and calculating volumes.
For best results, manure should be sampled at the time of application or as close as possible to
application. Sampling during application will help to ensure that samples are well-mixed and
representative of the manure being applied. Because manure nutrient analysis typically takes
several days at a lab, sampling at the time of application will not provide immediate manure
nutrient recommendations. The results can, however, be used for subsequent manure applications and to adjust commercial fertilizer application. This is why it is important to develop a
manure sampling history and use those analyses in a nutrient management plan. A manure
sampling history will also help you recognize if unplanned changes have occurred to your
system if management and other factors have remained constant. A manure sampling history
will give you confidence in using manure, and show you how consistent nutrient concentration
is from year to year.
Take manure samples annually for three years for new facilities, followed with samples every
three to five years, unless animal management practices, feed rations, or manure handling and
storage methods change drastically from present methods. If you apply manure several times a

PM 1558

Revised November 2003

O-116
year, take samples when you plan to apply the bulk of
manure. For example, it may be appropriate to sample in the
spring when manure that has accumulated all winter will be
applied. If storages are emptied twice a year, it may be
necessary to sample in both spring and fall since the different
storage temperatures in summer versus winter will affect
manure nutrient levels. NOTE: Implementation of future
federal regulations may require concentrated animal feeding
operations (> 1,000 animal units) to sample annually. Please
check state and federal requirements to determine sampling
frequency.

How to Sample
Semi-Solid or Liquid Manure
In liquid and semi-solid systems, settled solids can contain
over 90 percent of the phosphorus (P), so complete agitation
is needed to accurately sample the entire storage if all the
manure in the storage structure is going to be applied. If,
however, solids will purposely be left on the bottom of the
storage structure when the manure is pumped out, as is
sometimes the case with lagoons, then complete agitation
during sampling may generate artificially high nutrient values.
In this case agitation of the solids or sludge on the bottom of a
lagoon is not needed for nutrient analysis.
Liquid manure is best sampled during land application, for it
is potentially more difficult and dangerous to sample from
liquid storage facilities than dry manure systems. When
sampling manure during application is not possible, or preapplication analysis is desired for determining rates, refer to
the section on sampling from a storage facility. If sampling
from a liquid storage facility, use caution to prevent accidents,
such as falling into the manure storage facility or being
overcome with hazardous gases produced by manure. Have
two people present at all times. Never enter confined manure
storage spaces without appropriate safety gear such as a selfcontained breathing apparatus.
Ideally, liquid manure should be agitated so a representative
sample can be obtained for laboratory analysis. When agitating a storage pit below a building, be sure to provide adequate
ventilation for both animals and humans. When agitating
outdoor unformed pits, monitor activities closely to prevent
erosion of berms or destruction of pit liners.

Liquid Manure Sample Preparation

All liquid samples should be handled as follows:
• Prior to sampling label a plastic bottle with your name,
date and sample identification number using a waterproof
pen.
• If the sample cannot be mailed or transported to a laboratory within a few hours, it should be frozen. Place the
container in a tightly sealed plastic bag and keep it cold
or frozen until it arrives at the laboratory.
• Most manure analysis laboratories do have plastic bottles
available for sample collection. Do not use glass containers, as expansion of the gases in the sample can cause the
container to break.

Liquid Manure Sampling
During Land Application

Liquid Manure Applied with Tank Wagons

• Since settling begins as soon as agitation stops, samples
should be collected as soon as possible after the manure
tank wagon is filled unless the tanker has an agitator.
• Immediately after filling the tank wagon, use a clean
plastic pail to collect manure from the loading or unloading port or the opening near the bottom of the tank. Be

sure the port or opening does not have a solids accumulation from prior loads.
• Use a ladle to stir the sample in the bucket to get the
solids spinning in suspension. While the liquid is
spinning remove a ladle full and carefully pour in the
sample bottle. See Figure 1.
• Repeat this procedure and take another sample until the
sample bottle is three-quarters full (Make sure the
manure solids have not settled to the bottom of the
bucket as each ladle is extracted; it is important to
include the solids in
the sample). Screw
the lid on tightly.

Liquid Manure
Applied by
Irrigation
Systems

• Place catch pans or
buckets randomly in
the field to collect
liquid manure that is
Figure 1. Collecting a liquid manure
applied by an irrigasample.
tion system. Inexpensive aluminum roasting
pans or plastic buckets can be used as catch pans. Use
several pans at different distances from the sprinkler
head.
• Immediately after the manure has been applied, collect
manure from catch pans or buckets and combine the
manure in one bucket to make one composite sample.
• Use a ladle to stir the sample in the bucket. While the
liquid is spinning remove a ladle full and carefully pour
into a sample bottle. See Figure 1.
• Repeat this procedure and take another sample until the
sample bottle is three-quarters full. Screw the lid on
tightly.

Liquid Manure Sampling
from Storage Facilities

For best sampling results, samples should be taken with a
sampling probe or tube (see Figure 2). Probes can be constructed out of 1.5-inch diameter PVC pipe. Cut the PVC pipe
a foot longer than the depth of the pit. Run a 1/4 -inch rod or
string through the length of the pipe and attach a plug such as
a rubber stopper or rubber ball (see Figure 3). The rod or the
string must be longer than the pipe. If using a rod, bend the
top over to prevent it from falling out of the pipe.
• Insert the pipe slowly into the pit or lagoon, with the
stopper open, to the full depth of the pit.
• Pull the string or rod
to close the bottom of
the pipe and extract the
vertical profile sample
inside the pipe (be
careful not to tip the
pipe and dump the
sample).
• Release the sample
carefully into a bucket.
• Repeat the process at
least three times around
the pit or lagoon
creating a composite
sample in the bucket.
• Use a ladle to stir the
sample in the bucket to
get the solids spinning
Figure 2. Sampling earthen basin
in suspension. While
with sampling probe.
the liquid is spinning,

O-117
take a ladle full and
carefully pour into a
sample bottle.
• Repeat again and
take another sample
until sample bottle
is three-quarters
full. Make sure the
manure solids have
not settled to the
bottom of the
Figure 3. Rubber stopper attached
bucket as each
to a metal rod to serve as a
dipper is extracted;
stopper for PVC manure sampling
it is important to
tube.
include the solids in
the sample. Screw the lid on tightly.

Pre-Sampling Nitrogen and
Potassium from Liquid Manure

If the procedures described above for sampling liquid manure
are impractical due to lack of sampling equipment, or the
inability to agitate the manure, manure samples can be dipped
off the top of stored liquid manure to analyze for N and K
concentrations. Research has shown that top-dipped liquid
samples represent approximately 90 percent of the N concentration measured in mixed, field-collected samples. Multiply
the results of the N concentration from top-dipped samples by
1.1 for a better estimate of the N concentration of the liquid
storage facility. Dipping a sample from the surface of a liquid
storage pit does NOT provide a good estimate of P concentration in the pit and is not recommended.

How to Sample
Dry or Solid Manure
In solid manure handling systems, many of which include
bedding, the proportions of fecal matter, urine, and bedding
will vary from one location to another within sites, and often
from season to season as well. It is necessary to take samples
from various places in the manure pile, stack, or litter to
obtain a representative sample for analysis. It may even be
beneficial to sample several times per year based on the
bedding content.
Manure sampling is best done in the field as manure is
applied. This ensures that losses that occur during handling,
storage, and application are taken into account and that
manure is better mixed, reducing stratification found during
sampling storage facilities. As with field sampling of liquid
manure, results will not be available in time to adjust current
application rates. However, sampling during application will
still allow producers to adjust any planned future commercial
fertilizer rates and manure application in subsequent years.
The following method describes a procedure for collecting dry
or solid manure samples from the field.

Dry Manure Sampling
During Land Application

Collect manure samples according to the following field
sampling procedure.
• Spread a sheet of plastic or tarp on the field. A 10-feet-by10-feet sheet works well for sampling manure.
• Fill the spreader with a load of manure.
• Drive the tractor and manure spreader over the top of the
plastic to spread manure over the sheet.
• Collect subsamples as described below (Steps 1-3, Com-

posite Sample Collection).
• Samples should be collected to represent the first, middle
and last part of the storage facility or loads applied and
should be correlated as to which loads are applied on
certain fields to track changes in nutrient concentrations
throughout the storage facility.

Sampling from Dry or Solid
Storage Facilities and Open Lots

Manure should be sampled at the time of application, but if
time and management practices prevent this, manure samples
can be collected from the storage facility. Sampling from
storages is not generally recommended due to difficulty in
collecting a representative sample. Although solid manure
storages are generally not fully enclosed and gases are somewhat diluted, always exercise caution when sampling from
storage facilities. If you have to enter a confined storage
facility, follow the safety recommendations described previously in the section on sampling liquid manure storages.

Open Paved Lots

Manure that accumulates on paved feedlots and is scraped
and hauled to the field is classified as scrape-and-haul feedlot
manure. Manure is usually removed from the feedlot daily or
several times a week.
• Collect manure by scraping a shovel across approximately
25 feet of the paved feedlot. This process should be
repeated ten or more times, taking care to sample in a
direction that slices through the large-scale variations of
moisture, bedding, depth, age, etc. (See Figure 4). Avoid
manure that is excessively wet (near waterers) or contains
unusual amounts of feed and hay.
• Use the shovel to thoroughly mix manure by continuously
scooping the outside of the pile to the center of the pile.
• Collect subsamples from this pile using the hand-in-bag
method that is
described below
(Steps 1-3 Composite
Sample Collection).
• This may need to be
done several times to
collect several
composite samples
for analysis.
Figure 4. Sampling a feed-lot for
manure sample.

Barn Gutter

Manure that accumulates in a barn or
housing facility, is temporarily stored in a gutter, and then
removed by a barn cleaner is classified as barn gutter manure.
Manure is usually removed from the barn once or twice daily.
• Shovel a vertical “slice” of manure from the gutter, making
sure the shovel reaches to the bottom of the gutter.
• Remove manure from the gutter and pile it on the barn
floor. Mix the manure with a shovel or pitchfork to
ensure that bedding is mixed thoroughly with manure.
When collecting samples from a gutter, be sure to include
the liquid that accumulates in the gutter’s bottom. Discard
foreign material and also take care not to add large
amounts of barn lime.
• Repeat steps one and two from various locations along the
gutter.
• Mix each pile thoroughly and collect subsamples from
each pile using the hand-and-bag method that is described below (Steps 1-3, Composite Sample Collection).

Dry Stack and Manure with Litter

Manure that is stored outside in a solid waste storage facility,
such as a stacking shed or horizontal concrete silo located
above ground, is classified as a dry stack. These facilities are
usually covered to prevent the addition of extra water. Dry

O-118
manure with litter should also be sampled in the following
manner.
• Remove manure from 10 to 20 locations throughout the
dry stack and place it in a pile using a pitchfork or shovel.
Manure should be collected from the center of the stack
as well as from near the outside walls, to get samples that
represent all ages and moisture levels of manure in the
stack. A bucket loader can cut a path into the center of
the pile to provide access for sampling. Subsamples
should be collected to the depth the litter will be removed
for application.
• Thoroughly mix manure with the shovel by continuously
scooping the outside of the pile to the center of the pile.
• Collect a composite manure sample as described below
(Steps 1-3, Composite Sample Collection).

Composite Sample Collection
for Dry or Solid Samples

1. Whether collecting from a plastic tarp in the field, a
feedlot, a storage facility, or a barn, sample in a grid
pattern so that all areas are represented. Combine 10 to
20 subsamples in a bucket or pile and mix thoroughly.
More subsamples will produce more accurate results and
are often required to produce a composite that best
represents nutrient levels.
2. The final composite sample that will be submitted for
nutrient analysis should be collected using the hand-inbag method. To collect a composite sample from the
mixed subsamples, place a one-gallon resealable freezer
bag turned inside out over one hand. With the covered
hand, grab a representative handful of manure and turn
the freezer bag right side out over the sample with the
free hand. Be careful not to get manure in the sealable
tracks.
3. Squeeze excess air out of the bag, seal, and place it in another plastic bag to prevent leaks. Label the bag with your
name, date, and sample identification number with a waterproof pen and freeze it immediately to prevent nutrient
losses and minimize odors. For manure with a high degree
of variability, multiple samples may need to be analyzed.
Manure samples should be mailed or delivered to the laboratory as soon as possible after sampling.
Manure samples should be sent to a lab for chemical analysis
as quickly as possible to avoid nutrient losses. For a list of
commercial laboratories, please call your ISU Extension office
or visit the Web at: http://extension.agron.iastate.edu/immag/
sp.html.

Table 1. Conversion Factors
To switch from
mg/l
ppm
ppm
ppm
ppm
lb/1,000 gal
lb/ton
percent
percent
percent
P (elemental)
K (elemental)

Multiply by
1.0
0.0001
0.00834
0.002
0.2265
0.012
0.05
83.4
20.0
2265
2.29
1.2

To get
ppm
percent
lb/1,000 gal
lb/ton
lb/acre-inch
percent
percent
lb/1,000 gal
lb/ton
lb/acre-inch
P2 O 5
K 2O

Additional Information
and Resources
Basic manure analyses determined by laboratories include
total nitrogen, total phosphorus, and total potassium. Results
from commercial laboratories are presented either as a percent
of the sample weight, as pounds per ton, as pounds per 1,000
gallons of manure, or in parts per million (ppm). Table 1
shows factors used to convert between measurements.
Usually, nutrients are expressed as N, P2O5, or K2O on a wet or
“as received” basis, but some labs may instead report data on
an elemental (P instead of P2O5, K instead of K2O) or dry
(without water) basis; so, be sure to confirm the units. In any
case, manure values from commercial laboratories express
nutrients as the total amount of nutrient in the manure
sample. Some primary nutrients, such as N and P, may not be
completely available for plant growth the first year manure is
applied. A portion of some nutrients present in manure are in
an organic form and unavailable for immediate plant uptake.
Organic forms require transformation to an inorganic form to
be available for plant uptake. This transformation is dependent on temperature, moisture, chemical environment, and
time. Availability of nutrients can be limited by field losses,
which are affected by the type of manure and by manure
application methods. These losses are not accounted for in
laboratory results. Refer to the ISU Extension publication
Managing Manure Nutrients for Crop Production (PM 1811) for
nutrient availability estimates and losses due to types of
manure application methods.
PM 1518k Manure Storage Poses Invisible Risks
PM 1941 Calibration and Uniformity of Solid Manure Spreaders
(12/03)
PM 1948 Calibrating Liquid Manure Applicators (02/04)
PM 1811 Managing Manure Nutrients for Crop Production
Additional resources may be found on the Iowa Manure Management Action Group (IMMAG) Web page at:
http://extension.agron.iastate.edu/immag/default.htm
Prepared by Angela Rieck-Hinz, extension program specialist,
Dept. of Agronomy; Jeffery Lorimor, associate professor, and Tom
L. Richard, associate professor, Dept. of Agricultural and
Biosystems Engineering and Kris Kohl, ISU field specialist- Agricultural Engineering.
Photos submitted by John Sawyer, Kris Kohl, Joel DeJong, Jeff
Lorimor and Charles Wittman
Reviewed by: John Sawyer, ISU; Chris Murray, Iowa Natural
Resources Conservation Service and Marty Schwager, Iowa Pork
Producers Association.

File: Agronomy 7-4
.
. . and justice for all
The U.S. Department of Agriculture (USDA) prohibits discrimination in all its programs
and activities on the basis of race, color, national origin, gender, religion, age,
disability, political beliefs, sexual orientation, and marital or family status. (Not all
prohibited bases apply to all programs.) Many materials can be made available in
alternative formats for ADA clients. To file a complaint of discrimination, write USDA,
Office of Civil Rights, Room 326-W, Whitten Building, 14th and Independence Avenue,
SW, Washington, DC 20250-9410 or call 202-720-5964.
Issued in furtherance of Cooperative Extension work, Acts of May 8 and June 30, 1914,
in cooperation with the U.S. Department of Agriculture. Stanley R. Johnson, director,
Cooperative Extension Service, Iowa State University of Science and Technology,
Ames, Iowa.

O-119

NPDES Permit Writers’ Manual for CAFOs

Appendix C. Historic Properties Requirements
Coverage under this permit is available only if your CAFO discharges and discharge- related
activities meet one of the eligibility criteria below:
Criterion A. Your CAFO discharges do not have the potential to have an effect on historic
properties and you are not constructing or installing new control measures on your site
that cause subsurface disturbance.
Criterion B. Your discharge-related activities (i.e., construction and/or installation of
control measures that involve subsurface disturbance) will not affect historic properties.
Criterion C. Your CAFO discharges and discharge-related activities have the potential
to have an effect on historic properties; you have consulted with the State Historic
Preservation Officer (SHPO), Tribal Historic Preservation Officer (THPO), or other tribal
representative regarding measures to mitigate or prevent any adverse effects on historic
properties; and, you have either (1) obtained and are in compliance with a written
agreement that outlines all such measures, or (2) been unable to reach agreement on such
measures.
Criterion D. You have contacted the SHPO, THPO, or other tribal representative and EPA in
writing informing them that you have the potential to have an effect on historic properties
and you did not receive a response from the SHPO, THPO, or tribal representative within
30 days of receiving your letter.
If you have been unable to reach agreement with a SHPO, THPO, or other tribal representative
regarding appropriate measures to mitigate or prevent adverse effects, the permitting authority
may notify you of additional measures you must implement to be eligible for coverage under this
permit.
CAFO operators must determine whether their permit-related activities have potential to affect a
property that is either listed or eligible for listing on the National Register of Historic Places. CAFO
operators must contact the SHPO, THPO, and/or any Indian tribe that attaches religious and
cultural significance to historic properties that may be affected. In instances where a Tribe does
not have a THPO, CAFO operators should contact the appropriate Tribal government office.

Appendix O: Sample Site-Specific NPDES General Permit
Appendix C. Historic Properties Requirements

O-120

NPDES Permit Writers’ Manual for CAFOs

Appendix D. Notice of Termination
(Insert Notice of Termination (NOT) Form or
Appropriate State Form)

Appendix O: Sample Site-Specific NPDES General Permit
Appendix D. Notice of Termination

NPDES Permit Writers’ Manual for CAFOs

Appendix

P

Sample Nutrient
Management Plan
This sample Nutrient Management Plan (NMP) is based on a hypothetical facility. The
accompanying photograph does not portray a facility on which this sample NMP is based. Nor do
the technical standards used to develop this sample NMP constitute a technical standard that the
U.S. Environmental Protection Agency (EPA) has reviewed for consistency with the requirements
of Title 40 of the Code of Federal Regulations (CFR) part 412.4(c)(2). EPA is using this sample NMP
for the purpose of demonstrating how to identify terms of the NMP as required for a confined
animal feeding operation (CAFO) permit pursuant to 40 CFR part 122.42(e)(5). Circulation of
this sample NMP and the technical standards therein does not constitute an endorsement of
the technical standards or the NMP’s approach toward managing nutrients. This sample NMP
is intended for educational purposes only and does not create or remove any legal rights or
requirements on any member of the public, states, or any other federal agency.
The following output was generated by using the Manure Management Planner, which is at

http://www.agry.purdue.edu/mmp/

NPDES Permit Writers’ Manual for CAFOs

P-1

NPDES Permit Writers’ Manual for CAFOs

Nutrient Management Plan
Farm contact information:

DEF Feedlot
c/o John Doe
xxx Ave.
Anytownin, IA 55555
515.555.5555

Latitude/Longitude:

Plan Period:

Oct 2009 - Sep 2014

Conservation Planner
As a Conservation Planner, I certify that I have reviewed both the Comprehensive Nutrient Management Plan
and Producer Nutrient Management Activities documents for technical adequacy and that the elements of the
documents are technically compatible, reasonable and can be implemented.
Signature:
Name:
Title:

SAMPLE _________________

Date:

N/A ______

Certification Credentials:

Conservation District
The Conservation District has reviewed the CNMP documents and concurs that the plan meets the District's
goals.
Signature:
Name:
Title:

SAMPLE_________________

Date:

N/A ______

Owner/Operator
As the owner/operator of this CNMP, I, as the decision maker, have been involved in the planning process
and agree that the items/practices listed in each element of the CNMP are needed. I understand that I am
responsible for keeping all the necessary records associated with the implementation of this CNMP. It is my
intention to implement/accomplish this CNMP in a timely manner as described in the plan.
Signature:
Name:

SAMPLE_________________

Date:

N/A _____

Appendix P: Sample Nutrient Management Plan
Page 2 of 41

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NPDES Permit Writers’ Manual for CAFOs

Contents
Section 1. Background and Site Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-3
1.1. General Description of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-3
1.2. Sampling and Equipment Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-4
1.3. Identified Resource Concerns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-4
Section 2. Manure and Wastewater Handling and Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-5
2.1. Map(s) of Production Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-5
2.2. Production Area Conservation Practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-5
2.3 Manure Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-5
2.4 Animal Inventory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-6
2.5. Normal Mortality Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-7
2.6. Planned Manure Exports off the Farm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-7
2.7. Planned Manure Imports onto the Farm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-7
Section 3. Farmstead Safety and Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-8
3.1. Emergency Response Plan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-8
3.2. Biosecurity Measures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-9
3.3. Catastrophic Mortality Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-9
3.4. Chemical Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-10
Section 4. Land Treatment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .P-11
4.1. Map(s) of Fields and Conservation Practices . . . . . . . . . . . . . . . . . . . . . . . . . . . P-11
4.2. Conservation Practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-11
Section 5. Soil and Risk Assessment Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-12
5.1. Soil Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-12
5.2. Predicted Soil Erosion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-12
5.3. Nitrogen and Phosphorus Risk Analysis – Iowa Phosphorus Index . . . . . . . . . . . . . . P-13
5.4. Additional Field Data Required by Risk Assessment Procedure . . . . . . . . . . . . . . . P-13
Section 6. Nutrient Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-14
6.1. Field Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-14
6.2. Manure Application Setback Distances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-14
6.3. Soil Test Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-14
6.4. Manure Nutrient Analysis(1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-14
6.5. Planned Crops and Fertilizer Recommendations . . . . . . . . . . . . . . . . . . . . . . . . P-15
6.6. Manure Application Planning Calendar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-15
6.7. Planned Nutrient Applications (Manure-spreadable Area) . . . . . . . . . . . . . . . . . . P-17
6.8. Field Nutrient Balance (Manure-spreadable Area) . . . . . . . . . . . . . . . . . . . . . . . P-18
6.9. Field Nutrient Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-19
6.10. Manure Inventory Annual Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-21
6.11. Fertilizer Material Annual Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-22
6.12. Whole-farm Nutrient Balance (Manure-spreadable Area ) . . . . . . . . . . . . . . . . . . P-22
Section 7. Record Keeping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-23
7.1. Land Application Equipment Inspections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-23
7.2. Record Keeping Forms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-23
7.3. Records Maintained in NMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-24
Section 8. Publications and References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-25
8.1. Publications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-25
8.2. Software and Data Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-25
8.3. Initialization Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-26

Appendix P: Sample Nutrient Management Plan

P-3

NPDES Permit Writers’ Manual for CAFOs

Section 1. Background and Site Information
1.1. General Description of Operation
Management
DEF Feedlots have been farming and operating this facility since 1978. The operation employs
a number of personnel on a full-time and seasonal basis driven by need. The cattle and crop
operations are handled as integrated systems. The crop operation complements the feedlot’s
feed and bedding requirements, and the manure generated by the feedlots provide nutrients for
the crops. At the time this plan was prepared, there are no plans for expansion during the period
covered by the plan.
This NMP has been prepared and is being implemented in compliance with state permit: [Identified
in Appendix O of this Manual]. This five-year plan will be updated as necessary and revised and
resubmitted when the permit is renewed in 2015.
Manure is handled in both solid and liquid (irrigated) forms and is distributed to crop production
areas. Manure generated by the feedlots in excess of crop production needs and land availability
during the growing season will be stockpiled within the footprint of the production area in a
manner that is compliant with all permit requirements. Collected and stored runoff from the
feedlots is planned to be used to irrigate crops to address peak water needs.

Animals
The feedlot permit is for 5,000 head of beef cattle on an 80.9-acre open feedlot. This plan covers
feeder cattle of all weights and sexes arriving to be fed to heavier weights (harvest).

Facilities
Open feedlot penning is employed in this feedlot, with baled cornstalk and soybean residue added
as bedding during inclement weather. Fence line feeding systems are filled with daily formulated
rations from a mixer/scale delivery vehicle. Stationary fountains provide fresh drinking water. A visual
inspection of all water lines is conducted daily.
All solids settling basins have been designed by a licensed engineer and approved by IDNR. Design
documentation is kept on file at the operation. Weekly operation and maintenance assessments and
required repairs will be conducted on all pens, settling basins, and associated equipment. Weekly
inspections are conducted and documented for all manure and process wastewater holding areas to
monitor available capacity.

Crop Fields
All land areas in this plan is either owned or rented and under the control of DEF Feedlots. There
are 1,237 tillable acres with planned continuous corn and corn/soybean rotations. Yield goals
are developed in accordance with Appendix A9: Chapter 567-- 65.17(6) Rules for Animal Feeding
Operations. In accordance with the technical standard, optimum crop yield determinations allow for
a crop yield increase of 10 percent. For the location of DEF Feedlots the average plus a 10% yield for
corn is 195 bushels/acre and for soybeans is 61 bushels/acre. The plan includes a cropping plan for
each field along with soil test results. (Please note that for ease of publication, the sample plan provides
this information for Field 8 only.)

Appendix P: Sample Nutrient Management Plan
Section 1. Background and Site Information

P-4

NPDES Permit Writers’ Manual for CAFOs

Land Application of Nutrients
The cropping pattern is a continuous corn and corn/soybean rotation. That allows for any residual
nitrogen from the soybean crop to be accounted for in the corn year. Manure is planned to be
applied at a rate that supplies two or four years of phosphorus depending on the outcome of the
required field-specific Phosphorus Index Risk Assessment. It is planned to apply the manure on
a priority basis to fields that have been harvested as corn, corn silage, baled residue or soybean
stubble. Actual manure distribution will take into account soil test, crop yields and uptake, ambient
weather conditions; manure stockpiled, soil moisture conditions, manure analyses and growing
crop production. Management strategies that will continue to evolve over the planning period will
include crop rotation, feed management, tillage practices, conservation practice and treatments,
seed varieties, pest management, and water conservation. All management adjustments will comply
with permit requirements and any applicable state and federal regulations.

1.2. Sampling and Equipment Calibration
Manure sampling and testing frequency
Manure is analyzed annually for nutrient content of total nitrogen, phosphorus, potassium,
and percent moisture. An analysis is taken for each different source of manure being generated.
Manure samples are collected according to ISU Publication PM-1558 How to Sample Manure
for Nutrient Analysis. Samples are analyzed by AGSource Cooperative Services DBA AGSource
Belmond Labs.

Soil sampling and testing frequency
The minimum frequency for soil testing will be once during a four-year period. All soil samples
will be collected according to Iowa State University (ISU) for sampling methods based on soil
maps, management zones, or grid sampling. See ISU PM 287 Take a Good Sample to Help Make
Good Decisions. All soil tests will be analyzed by a soil test lab that is certified according to Iowa
Department of Agriculture and Land Stewardship (IDALS) soil test lab certification standards.
Before sampling, each field was broken into uniform sampling areas, as is determined by the
types of soils present, past management and productivity, and goals desired for field management
practices. In accordance with ISU PM 287, each of these sampling areas was 10 acres or less. A
total of 10–12 cores or borings per sampling area were taken and combined to form a composite
sample for each field.

Equipment calibration method and frequency
Equipment will be calibrated annually and records are maintained at the operation. For record
keeping requirements necessary for application equipment, see section 7.

1.3. Identified Resource Concerns
Where surface water or other sensitive areas are present in a field, setbacks are maintained during
manure and commercial nutrient distribution in accordance with permit requirements. The
primary resource concern to be managed under this plan is surface water runoff. Depending on
the specific needs of each field to address that concern, the plan identifies the specific practices to

Appendix P: Sample Nutrient Management Plan
Section 1. Background and Site Information

P-5

NPDES Permit Writers’ Manual for CAFOs

be employed to control surface water runoff. Those practices include terraces, grassed waterways,
contour farming, and residue management. Employee training is conducted regularly addressing
manure storage, manure handling, and distribution. Documentation of all training activities is
maintained at the operation. (Please note that for ease of publication, the sample plan provides this
information for Field 8 only.)

Section 2. Manure and Wastewater Handling and Storage
2.1. Map(s) of Production Area
To simplify publication of this sample plan, the production area map is not included. A production
area map should be included with all NMPs developed and implemented as a condition of a
National Pollutant Discharge Elimination System CAFO permit.

2.2. Production Area Conservation Practices
Clean water diversion
All clean rainwater is diverted away from the feedlot using grass covered swales and berms.
Vegetation will remain established in the grassed swale and grass swales will be mowed as
needed to ensure proper function. No clean water is collected. The production area will be
checked weekly to insure that clean rainwater continues to flow away from the feedlot. See
section 7 for record keeping requirements necessary for weekly inspections.

Measures to prevent direct contact of animals with water
Confined animals have no access to waters of the state in the production area.

2.3 Manure Storage
Type of Storage

Pumpable or Spreadable
Capacity

Annual Manure
Collected

E Lots Stack #1

Dry stack

2,199 Tons

4,375 Tons

E SetldSolidBasin #3

Dry stack

756 Tons

757 Tons

Storage ID

E Storage Pond #1

Earthen storage

16,502,043 Gal

10,575,180 Gal

W Lots Stack #2

Dry stack

879 Tons

1,750 Tons

W SetdSolidBasin#4

Dry stack

247 Tons

247 Tons

W Storage Pond #2

Earthen storage

3,112,645 Gal

5,876,413 Gal

Dry stacks are contained in the open feedlots. They are not covered and, therefore, are open to
direct precipitation. The wastewater runoff that is generated from the feedlots is collected. Solids
are settled in W SetdSolid Basin #4. The liquid is then diverted to W Storage Pond #2. W Storage
Pond #2 is connected to E Storage Pond #1. Land application of liquid manure is applied directly
from E Storage Pond #1.1

1

For simplicity only Field 8 is illustrated in this plan. Field 8S does not receive manure application from E Storage Pond #1.

Appendix P: Sample Nutrient Management Plan
Section 2. Manure and Wastewater Handling and Storage

P-6

NPDES Permit Writers’ Manual for CAFOs

The pumpable capacity represents the total design volume as calculated in the engineering
and design construction plans. Engineering design and construction plans for both types of
storage structures are not included as part of this NMP but are to be kept on-site. They include
calculations for
▶ The volume of manure, process wastewater, and other wastes accumulated during the
critical storage period.
▶ The volume of normal precipitation minus evaporation on the storage structure
surface.
▶ The volume of runoff from the facility’s drainage area from normal rainfall events,
which includes runoff from mortality area described in section 2.5.
▶ The volume of precipitation from the 25-year, 24-hour rainfall event on the storage
structure surface.
▶ The volume of runoff from the facility’s drainage area from the 25-year, 24-hour
rainfall event.
▶ The volume of any leachate from bunk silos or other silage storage areas.
▶ The volume of solids remaining in a storage structure after liquids are removed.
The 25-year, 24-hour storm for the location of the operation is 4.9 inches. The volume in E Storage
Pond #1 attributed for this size storm is 2,405,282 gallons. The critical storage volume is 14,096,761
gallons. A depth marker will be placed in E Storage Pond #1 identifying 14,096,761 gallons as the
upper pump down level. In addition, the storage pond contains an additional 2 feet of free board.

Operation and Maintenance
Manure will be land applied in accordance with this NMP, and solids will be removed at a
frequency necessary to maintain the storage capacity as described above.
All visual inspections will be conducted as outlined in section 7.3 of this NMP. Fencing will be
maintained around the perimeter of the ponds to prevent animal access.

2.4 Animal Inventory
Type or Production
Phase

Number of
Animals(1)

Average
Weight
(Lbs)

Confinement Period

Manure
Collected
(%)(2)

Cattle #1 basin

Finishing steer (beef)

2,500

850

Jan Early–Dec Late

30

E. Lots Stack #1

Cattle #1 dry stack

Finishing steer (beef)

2,500

850

Jan Early–Dec Late

60

W. SetldSolid Basin #4

Animal Group

Storage Where Manure
Will Be Stored

Cattle #1 pond

Finishing steer (beef)

2,500

850

Jan Early–Dec Late

10

E. Storage Pond #1

Cattle #2 basin

Finishing steer (beef)

2,500

850

Jan Early–Dec Late

30

E .SetldSolid Basin #3

Cattle #2 dry stack Finishing steer (beef)

2,500

850

Jan Early–Dec Late

60

W. Storage Pond #2

Cattle #2 pond

2,500

850

Jan Early–Dec Late

10

W. Lots Stack #2

Finishing steer (beef)

(1) Number of Animals is the average number of animals that are present in the production facility at any one time.
(2) If Manure Collected is less than 100%, this indicates that the animals spend a portion of the day outside of the production facility or that the production
facility is unoccupied one or more times during the confinement period.

Appendix P: Sample Nutrient Management Plan
Section 2. Manure and Wastewater Handling and Storage

P-7

NPDES Permit Writers’ Manual for CAFOs

2.5. Normal Mortality Management
To protect surface and groundwater resources, reduce the impact of odors that result from
improperly handled animal mortality, and decrease the likelihood of the spread of disease
or other pathogens, approved handling and utilization methods shall be implemented in the
handling of normal mortality losses.

Plan for Proper Management of Dead Animals
NRCS IA Standard 316, Animal Mortality Facility, October 2007 will be followed for proper
management of dead animals. Dead animals will be disposed of utilizing Valley Rendering
Services. When rendering services are used, dead animals should be picked up within 24 hours.
Dead animals will be stored in a separate bermed area adjacent to the production area to control
runoff. Adequate space is available in the bermed area to hold normal animal mortality at the
feedlot operation. Process wastewater that runs off that area is collected and transported to the
waste storage ponds. The liquid storage calculations account for this additional volume of liquid.
There are no additional operation and maintenance activities required with plan to be used to
address normal animal mortality at the operation. Under no circumstances will the manure
treatment systems be used to manage any mortality. Contact information for Valley Rendering is
(555)-555-5555.

2.6. Planned Manure Exports off the Farm
Month-Year

Manure Source

Amount

Receiving Operation

Location

During the period covered by the plan no manure is to be exported from the DEF Feedlots
operation.

2.7. Planned Manure Imports onto the Farm
Month-Year

Manure’s Animal Type

Amount

Originating Operation

Location

During the period covered by the plan, no manure is to be imported into the DEF Feedlots
operation.

Appendix P: Sample Nutrient Management Plan
Section 2. Manure and Wastewater Handling and Storage

P-8

NPDES Permit Writers’ Manual for CAFOs

Section 3. Farmstead Safety and Security
3.1. Emergency Response Plan
In Case of an Emergency Storage Facility Spill, Leak or Failure
Implement the following first containment steps:
a. Stop all other activities to address the spill.
b. Stop the flow. For example, use skid loader or tractor with blade to contain or divert
spill or leak.
c. Call for help and excavator if needed.
d. Complete the clean-up and repair the necessary components.
e. Assess the extent of the emergency and request additional help if needed.
In Case of an Emergency Spill, Leak or Failure during Transport
or Land Application
Implement the following first containment steps:
a. Stop all other activities to address the spill and stop the flow.
b. Call for help if needed.
c. If the spill posed a hazard to local traffic, call for local traffic control assistance and
clear the road and roadside of spilled material.
d. Contain the spill or runoff from entering surface waters using straw bales, saw dust,
soil or other appropriate materials.
e. If flow is coming from a tile, plug the tile with a tile plug immediately.
f. Assess the extent of the emergency and request additional help if needed.
Emergency Contacts
Department / Agency

Phone Number

Fire

xxx-xxx-xxxx

Rescue services

xxx-xxx-xxxx

State veterinarian

xxx-xxx-xxxx

Sheriff or local police

xxx-xxx-xxxx

Appendix P: Sample Nutrient Management Plan
Section 3. Farmstead Safety and Security

P-9

NPDES Permit Writers’ Manual for CAFOs

Nearest available excavation equipment/supplies for responding to emergency
Equipment Type

Contact Person

Phone Number

xxxxx

John Doe

xxx-xxx-xxxx

Contacts to be made by the owner or operator within 24 hours
Organization

Phone Number

EPA Emergency Spill Hotline

xxx-xxx-xxxx

County Health Department

xxx-xxx-xxxx

Other State Emergency Agency

xxx-xxx-xxxx

Be prepared to provide the following information:
a. Your name and contact information.
b. Farm location (driving directions) and other pertinent information.
c. Description of emergency.
d. Estimate of the amounts, area covered, and distance traveled.
e. Whether manure has reached surface waters or major field drains.
f. Whether there is any obvious damage: employee injury, fish kill, or property damage.
g. Current status of containment efforts.

3.2. Biosecurity Measures
Biosecurity is critical to protecting livestock and poultry operations. Standard operating
procedures at DEF Feedlots require all visitors to check in with the facility manager before
entering the operation or any production or storage facility. This procedure is included in the
content of the training program given to all employees.

3.3. Catastrophic Mortality Management
In the case of catastrophic mortality on-farm disposal will be conducted if site conditions permit.
On-farm methods typically include burial, composting, and incineration. The extent of mortality
and specific state requirements will dictate the practice to be used. Catastrophic mortality will be
addressed in a manner that is protective of surface and groundwater quality and human health.
Activities will be conducted in accordance with all applicable state and local laws, regulations,
and guidelines. Under no circumstances will the manure treatment systems be used to manage
any mortalities.
Important! In the event of catastrophic animal mortality, contact the permitting authority before
beginning carcass disposal.

Appendix P: Sample Nutrient Management Plan
Section 3. Farmstead Safety and Security

P-10

NPDES Permit Writers’ Manual for CAFOs

3.4. Chemical Handling
If checked, the indicated measures will be taken to prevent chemicals and other contaminants
from contaminating process waste water or storm water storage and treatment systems.
Measure
This is not a regulatory-agency permitted facility. This section does not apply.
x

All chemicals are stored in proper containers. Expired chemicals and empty containers
are properly disposed of in accordance with state and federal regulations. Pesticides and
associated refuse are disposed of in accordance with the FIFRA label.

x

Chemical storage areas are self-contained with no drains or other pathways that will allow
spilled chemicals to exit the storage area.

x

Chemical storage areas are covered to prevent chemical contact with rain or snow.

x

Emergency procedures and equipment are in place to contain and clean up chemical
spills.

x

Chemical handling and equipment wash areas are designed and constructed to prevent
contamination of surface waters and waste water and storm water storage and treatment
systems.
All chemicals are custom applied and no chemicals are stored at the operation. Equipment
wash areas are designed and constructed to prevent contamination of surface waters and
waste water and storm water storage and treatment systems.

Appendix P: Sample Nutrient Management Plan
Section 3. Farmstead Safety and Security

P-11

NPDES Permit Writers’ Manual for CAFOs

Section 4. Land Treatment
4.1. Map(s) of Fields and Conservation Practices
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)

4.2. Conservation Practices
The following conservation practices have been integrated with crop production practices at the
DEF feedlots to control runoff and protect water quality. The specific practices being utilized in
each field incorporated into this plan are specified in the table below. The table includes the NRCS
conservation practice standard that dictates the implementation and management protocols
that are to be employed during the planning period. (Please note that for ease of publication, the
sample plan provides this information for Field 8 only.)

Appendix P: Sample Nutrient Management Plan
Section 4. Land Treatment

P-12

NPDES Permit Writers’ Manual for CAFOs

Field

Area

Conservation Practice

NRCS Iowa Conservation Practice Reference

Bob’s Farm North – 8N

56.4 Acres

50ꞌ Stream Vegetated Buffer

Riparian Forest Buffer (Ac.) (391)
(August 2007)

Contour Farming

Contour Farming (Ac.) (330) (May 2005)

Residue Management

Residue Management, Seasonal (Ac.) (344)
(March 2007)

50ꞌ Stream Vegetated Buffer

Riparian Forest Buffer (Ac.) (391)
(August 2007)

Contour Farming

Contour Farming (Ac.) (330) (May 2005)

Residue Management

Residue Management, Seasonal (Ac.) (344)
(March 2007)

Bob’s Farm South – 8S

79.6 Acres

Section 5. Soil and Risk Assessment Analysis
5.1. Soil Information
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)
Soil
Slope
Component Surface Range
Name
Texture
(%) Drainage

Hydro­
logic
Group

Perm. Subsoil Subsoil
Code
P
K
Texture

Soil
Survey

Map
Unit

Bob’s Farm North – 8N

167

1C3

Ida

SIL

5-9%

Well

B

50

Low

Low

Fine

44

Bob’s Farm South – 8S

167

1C3

Ida

SIL

5-9%

Well

B

50

Low

Low

Fine

44

Field

CSR

5.2. Predicted Soil Erosion
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)
Predominant
Soil Type

Slope
(%)

Bob’s Farm North – 8N

1C3 (Ida SIL)

7.0

3.1

Bob’s Farm South – 8S

1C3 (Ida SIL)

7.0

3.9

Field

Field
Bob’s Farm North – 8N

Bob’s Farm South – 8S

Wind
(Ton/Ac/Yr)

Irrigation
(Ton/Ac/Yr)

Ending Date
(mm/dd/yyyy)

Gully
(Ton/Ac/Yr)

Soil Loss
(Ton/Ac)

Ephemeral
(Ton/Ac/Yr)

Crop Year

Starting Date
(mm/dd/yyyy)

2010

10/23/2009

10/10/2010

2.0

Soybean

2011

10/11/2010

10/22/2011

4.2

Corn

2012

10/23/2011

10/10/2012

3.6

Soybean

Primary Crop

2013

10/11/2012

10/20/2013

2.9

Corn

2014

10/21/2013

10/10/2014

2.6

Soybean

2010

10/23/2009

10/10/2010

2.0

Soybean

2011

10/11/2010

10/22/2011

3.7

Corn

2012

10/23/2011

10/10/2012

3.6

Soybean

2013

10/11/2012

10/20/2013

5.7

Corn

2014

10/21/2013

10/10/2014

4.4

Soybean

Appendix P: Sample Nutrient Management Plan
Section 5. Soil and Risk Assessment Analysis

Plan Avg. Soil
Loss (Ton/Ac/Yr)

P-13

NPDES Permit Writers’ Manual for CAFOs

5.3. Nitrogen and Phosphorus Risk Analysis – Iowa Phosphorus Index
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)
Crop Year

Erosion
Component

Runoff
Component

Drainage
Component

P Index
w/o P Apps

P Index
w/ P Apps

Bob’s Farm North – 8N

2010

1.05

0.21

0.00

1.26

1.26

Low

Bob’s Farm North – 8N

2011

2.21

0.21

0.00

2.42

2.42

Medium

Bob’s Farm North – 8N

2012

1.90

0.22

0.00

2.10

2.11

Medium

Bob’s Farm North – 8N

2013

1.53

0.22

0.00

1.73

1.74

Low

Bob’s Farm North – 8N

2014

1.37

0.24

0.00

1.58

1.61

Low

Bob’s Farm South – 8S

2010

1.07

0.23

0.00

1.29

1.29

Low

Bob’s Farm South – 8S

2011

1.97

0.23

0.00

2.20

2.20

Medium

Bob’s Farm South – 8S

2012

1.92

0.34

0.00

2.15

2.26

Medium

Bob’s Farm South – 8S

2013

3.04

0.34

0.00

3.27

3.37

Medium

Bob’s Farm South – 8S

2014

2.35

0.34

0.00

2.57

2.68

Medium

Field

P Loss Risk

5.4. Additional Field Data Required by Risk Assessment Procedure
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)
Sediment
Type of
Trap
Artificial Conservation
Drainage
Practice

Distance
to Water
(Feet)

Buffer
Width
(Feet)

Bob’s Farm North – 8N

500

None

None

None

Northwest Iowa
Plains

Tillage Used

Row crops - SR +
CR, good

Bob’s Farm South – 8S

500

None

None

None

Northwest Iowa
Plains

Tillage Used

Row crops - SR +
CR, good

Field

Landform Region

Residue
Management

Land Use

Appendix P: Sample Nutrient Management Plan
Section 5. Soil and Risk Assessment Analysis

P-14

NPDES Permit Writers’ Manual for CAFOs

Section 6. Nutrient Management
6.1. Field Information
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)
Spreadable
Acres

FSA
Farm

FSA
Tract

FSA
Field

Total
Acres

Bob’s Farm North – 8N

8N

56.4

1C3 (Ida SIL)

7.0

Bob’s Farm South – 8S

8S

79.6

1C3 (Ida SIL)

7.0

County

Predominant
Soil Type

Slope
(%)

Sub-field
ID

Field ID

6.2. Manure Application Setback Distances
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)
Field

Setback Distance

Bob’s Farm North – 8N

There are no surface waters or other sensitive features present in this field that require manure
application setback. A stream is present in the land area between field 8N and 8S, and a 50-foot
vegetated buffer is maintained where there is no manure application

Bob’s Farm South – 8S

There are no surface waters or other sensitive features present in this field that require manure
application setback. A stream is present in the land area between field 8N and 8S, and a 50-foot
vegetated buffer is maintained where there is no manure application

6.3. Soil Test Data
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)
Field

Test Year

OM (%)

P Test
Used

P

K

Mg

Ca

Units

Soil pH

Buffer
pH

CEC
(meq/100g)

Bob’s Farm North – 8N

2009

3.1

Bray P1

28

221

390

2,208

ppm

7.0

7.0

14.9

Bob’s Farm South – 8S

2009

3.0

Bray P1

32

196

418

1,941

ppm

6.8

7.0

13.7

6.4. Manure Nutrient Analysis(1)
Manure Source

Dry
Matter (%) Total N

NH4 -N

Total
P 2 O5

Total
K 2O

Avail.
P2O5(2)

Avail.
K 2O(2)

Units

Analysis Source and Date

E Lots Stack #1

7.0

2.6

10.0

14.0

10.0

14.0

Lb/Ton

Mid West Labs

E SetldSolidBasin #3

7.9

2.9

2.9

8.8

2.9

8.8

Lb/Ton

Mid West Labs

E Storage Pond #1

1.7

1.0

0.5

3.0

0.5

3.0

W Lots Stack #2

7.0

2.6

10.0

14.0

10.0

14.0

Lb/Ton

Mid West Labs

W SetdSolidBasin#4

7.9

2.9

2.9

8.8

2.9

8.8

Lb/Ton

Mid West Labs

W Storage Pond #2

1.7

1.0

0.5

3.0

0.5

3.0

Lb/1000Gal Mid West Labs

Lb/1000Gal Mid West Labs

(1) Entered analysis may be the average of several individual analyses.
(2) Iowa assumes that 100% of manure phosphorus and 100% of manure potassium is crop available. First-year per-acre nitrogen availability for individual
manure applications is given in the Planned Nutrient Applications table. For more information about nitrogen availability in Iowa, see “Managing
Manure Nutrients for Crop Production,” Iowa State Extension, PM 1811, Nov. 2003.

Appendix P: Sample Nutrient Management Plan
Section 6. Nutrient Management

P-15

NPDES Permit Writers’ Manual for CAFOs

6.5. Planned Crops and Fertilizer Recommendations
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)

Field

Crop
Year

Planned Crop

Bob’s Farm North – 8N

2010

Soybean

Bob’s Farm North – 8N

2011

Corn

Bob’s Farm North – 8N

2012

Soybean

Yield Goal
(per Acre)

N Rec
(Lbs/A)

P2O5 Rec
(Lbs/A)

K 2O Rec
(Lbs/A)

61.0 Bu

0

0

0

195.0 Bu

160

0

0

61.0 Bu

0

0

0

P 2 O5
Removed
(Lbs/A)

K 2O
Removed
(Lbs/A)

49

92

73

59

232

49

92

N Removed
(Lbs/A)
232

Bob’s Farm North – 8N

2013

Corn

195.0 Bu

160

0

0

73

59

Bob’s Farm North – 8N

2014

Soybean

61.0 Bu

0

0

0

232

49

92

Bob’s Farm South – 8S

2010

Soybean

61.0 Bu

0

0

0

232

49

92

195.0 Bu

160

0

0

73

59

61.0 Bu

0

0

0

232

49

92

195.0 Bu

160

0

0

73

59

61.0 Bu

0

0

0

49

92

Bob’s Farm South – 8S

2011

Corn

Bob’s Farm South – 8S

2012

Soybean

Bob’s Farm South – 8S

2013

Corn

Bob’s Farm South – 8S

2014

Soybean

232

Unharvested cover crop or first crop in double-crop system.
a Custom fertilizer recommendation.
*

6.6. Manure Application Planning Calendar
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)

October 2009 through September 2010

Field

Primary
2010 Crop
Pre­
(Prev.
Total Spread. dominant Primary
Crop)
Acres Acres Soil Type

Bob’s Farm North – 8N 56.4

56.4

Ida SIL
(1C3
5-9%)

Soybean
(Corn)

Bob’s Farm South – 8S 79.6

79.6

Ida SIL
(1C3
5-9%)

Soybean
(Corn)

Oct
'09

Nov
'09

Dec
'09

Jan
'10

Feb
'10

Mar
'10

Apr
'10

May Jun
'10 '10

Jul
'10

Aug Sep
'10 '10

Nov
'10

Dec
'10

Jan
'11

Feb
'11

Mar
'11

Apr
'11

May Jun
'11 '11

Jul
'11

Aug Sep
'11 '11

October 2010 through September 2011

Field

Primary
2011 Crop
Pre­
(Prev.
Total Spread. dominant Primary
Crop)
Acres Acres Soil Type

Oct
'10

Bob’s Farm North – 8N 56.4

56.4

Ida SIL
Corn
(1C3 (Soybean)
5-9%)

39.5

Bob’s Farm South – 8S 79.6

79.6

Ida SIL
Corn
(1C3 (Soybean)
5-9%)

100.9

Appendix P: Sample Nutrient Management Plan
Section 6. Nutrient Management

P-16

NPDES Permit Writers’ Manual for CAFOs

October 2011 through September 2012
Primary
2012 Crop
Pre­
(Prev.
Total Spread. dominant Primary
Crop)
Acres Acres Soil Type

Field

Bob’s Farm North – 8N 56.4

56.4

Ida SIL
(1C3
5-9%)

Soybean
(Corn)

Bob’s Farm South – 8S 79.6

79.6

Ida SIL
(1C3
5-9%)

Soybean
(Corn)

Oct
'11

Nov
'11

Dec
'11

Jan
'12

Feb
'12

Mar
'12

Apr
'12

May Jun
'12 '12

Jul
'12

Aug Sep
'12 '12

Nov
'12

Dec
'12

Jan
'13

Feb
'13

Mar
'13

Apr
'13

May Jun
'13 '13

Jul
'13

Aug Sep
'13 '13

Jul
'14

Aug Sep
'14 '14

October 2012 through September 2013
Primary
2013 Crop
Pre­
(Prev.
Total Spread. dominant Primary
Crop)
Acres Acres Soil Type

Field

Bob’s Farm North – 8N 56.4

56.4

Ida SIL
Corn
(1C3 (Soybean)
5-9%)

Bob’s Farm South – 8S 79.6

79.6

Ida SIL
Corn
(1C3 (Soybean)
5-9%)

Oct
'12

60.2

October 2013 through September 2014
Primary
2014 Crop
Pre­
(Prev.
Total Spread. dominant Primary
Crop)
Acres Acres Soil Type

Field

Bob’s Farm North – 8N 56.4

56.4

Ida SIL
(1C3
5-9%)

Soybean
(Corn)

Bob’s Farm South – 8S 79.6

79.6

Ida SIL
(1C3
5-9%)

Soybean
(Corn)

Slope > 10%

Oct
'13

Slope > 5% (Winter only)(1)

Nov
'13

Dec
'13

Jan
'14

Feb
'14

Mar
'14

Apr
'14

May Jun
'14 '14

50.4 3.2

Crop in field

No. indicates total loads
"X" indicates other
manure apps

Nutrients and organic nutrient sources shall not be surface applied to frozen, snow-covered ground, or saturated soil if a potential risk for runoff exists.
A potential risk for runoff exists on slopes greater than 5% unless erosion is controlled to soil loss tolerance levels (“T”) or less. Manure may be surface
applied to frozen, snow-covered or saturated ground if a potential risk for runoff exists only under one of the following conditions.
• Where manure storage capacity is insufficient and failure to surface apply creates a risk of an uncontrolled release of manure.
• On an emergency basis.
Manure surface applied to frozen, snow covered, or saturated ground shall be based on a manure disposal plan. That plan shall include:
• Under what circumstances the manure may be applied to frozen, snow covered, or saturated ground. (Ex: storage capacity exceeded).
• Rates of application.
• Area of application.
• Other requirements such as runoff control as indicated through the use of the Iowa Phosphorus Index assessment tool.
1)

Appendix P: Sample Nutrient Management Plan
Section 6. Nutrient Management

P-17

NPDES Permit Writers’ Manual for CAFOs

6.7. Planned Nutrient Applications (Manure-spreadable Area)
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)

Field

App.
Month

Target
Crop

Bob’s Farm
North – 8N

Nov
2010

Corn

Bob’s Farm
North – 8N

Nov
2010

Bob’s Farm
North – 8N

Loads,
Total
Avail Avail
Speed Amount Acres Avail N P2O5
K 2O
or Time Applied Cov. (Lbs/A) (Lbs/A) (Lbs/A)

Application
Method

Rate
Basis

Rate/
Acre

E
SetldSolidBasin
#3

Dry Box
Spreader,
Not
incorporated

2-yr P

10.5
Ton

28.4
Lds

426
Ton

40.6

20

30

92

Corn

W
SetdSolidBasin
#4

Dry Box
Spreader,
Not
incorporated

2-yr P

10.5
Ton

11.1
Lds

166.5
Ton

15.9

20

30

92

Apr
2011

Corn

28-0-0

Shallow
subsurface
band (<4")

Supp. N

47
Gal

2,651
Gal

56.4

140

0

0

Bob’s Farm
North – 8N

Apr
2013

Corn

28-0-0

Shallow
subsurface
band (<4")

1-yr N

41
Gal

2,312
Gal

56.4

122

0

0

Bob’s Farm
North – 8N

May
2013

Corn

E
Dry Box
SetldSolidBasin Spreader,
#3
incorp. w/in
7 day(s)

1-yr P

16
Ton

60.2
Lds

903
Ton

56.4

35

46

141

Bob’s Farm
North – 8N

Apr
2014

Soy­
E
Dry Box
bean SetldSolidBasin Spreader,
#3
incorp. w/in
7 day(s)

1-yr P

17
Ton

50.4
Lds

756
Ton

44.5

37

49

150

Bob’s Farm
North – 8N

May
2014

Soy­
bean

W
SetdSolidBasin
#4

Dry Box
Spreader,
incorp. w/in
7 day(s)

1-yr P

17
Ton

3.2
Lds

48
Ton

2.8

37

49

150

Bob’s Farm
South – 8S

Nov
2010

Corn E Lots Stack #1

Dry Box
Spreader,
Not
incorporated

3-yr P

19
Ton

100.9
Lds

1,514
Ton

79.7

32

190

266

Bob’s Farm
South – 8S

Apr
2011

Corn

28-0-0

Shallow
subsurface
band (<4")

Supp. N

43
Gal

3,423
Gal

79.6

128

0

0

Bob’s Farm
South – 8S

Apr
2013

Corn

28-0-0

Shallow
subsurface
band (<4")

1-yr N

53
Gal

4,219
Gal

79.6

158

0

0

Bob’s Farm
South – 8S

Sep
2014

Corn

W Lots Stack
#2

1,500
Ton

75.0

34

200

280

Nutrient Source

Dry Box
Custom
Spreader,
Not
incorporated

20
Ton

100
Lds

Appendix P: Sample Nutrient Management Plan
Section 6. Nutrient Management

P-18

NPDES Permit Writers’ Manual for CAFOs

6.8. Field Nutrient Balance (Manure-spreadable Area)
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)

Year

Field

Size
Acres

Crop

2010 Bob’s Farm
North – 8N

56.4 Soybean

2011 Bob’s Farm
North – 8N

56.4

2012 Bob’s Farm
North – 8N

56.4 Soybean

2013 Bob’s Farm
North – 8N

56.4

2014 Bob’s Farm
North – 8N

56.4 Soybean

Corn

Corn

Yield
Goal/
Acre

79.6 Soybean

2011 Bob’s Farm
South – 8S

79.6

2012 Bob’s Farm
South – 8S

79.6 Soybean

2013 Bob’s Farm
South – 8S

79.6

2014 Bob’s Farm
South – 8S

79.6 Soybean

Corn

Corn

N
Lb/A

P 2 O5
Lb/A

K 2O
Lb/A

N
Lb/A

P2O5
Lb/A

K 2O
Lb/A

Balance After Recs3

Balance After
Removal4

N
Lb/A

P 2 O5
Lb/A

P 2 O5
Lb/A

K 2O
Lb/A

K 2O
Lb/A

61

0

0

0

0

0

0

0

0

0

-49

-92

195

160

0

0

160

30

92

0

30

92

-43

33

61

0

0

0

0

0

0

0

30

92

-49

-59

195

160

0

0

157

46

141

0†

76

233

-27

82

61

0

0

0

31

41

126

0ª

117

359

-8

116

320

0

0

348

117

359

61

0

0

0

0

0

0

0

0

0

-49

-92

195

160

0

0

160

190

266

0

190

266

117

207

61

0

0

0

0

0

0

0

190

266

68

115

195

160

0

0

158

0

0

2†

190

266

-5

56

61

0

0

0

0

0

0

0

190

266

-49

-36

320

0

0

318

190

266

Total Bob’s Farm
North – 8N
2010 Bob’s Farm
South – 8S

Nutrients Applied2

Fertilizer Recs1

Total Bob’s Farm
South – 8S

1 Fertilizer Recs are the crop fertilizer recommendations. The N rec accounts for any N credit from previous legume crop.
2 Nutrients Applied are the nutrients expected to be available to the crop from that year’s manure applications plus nutrients from that year’s commercial
fertilizer applications and nitrates from irrigation water. With a double-crop year, the total nutrients applied for both crops and the year's balances are
listed on the second crop’s line.
3 For N, Nutrients Applied minus Fertilizer Recs for indicated crop year. Also includes amount of residual N expected to become available that year from
prior years' manure applicaitions. For P2O5 and K 2O, Nutrients Applied minus Fertilizer Recs through the indicated crop year, with positive balances
carried forward to subsequent years. Negative values indicate a potential need to apply additional nutrients.
4 Nutrients Applied minus amount removed by harvested portion of crop through the indicated year. Positive balances are carried forward to subsequent
years.
¤ Indicates a custom fertilizer recommendation in the Fertilizer Recs column.
ª Indicates in the Balance After Recs N column that the legume crop is assumed to utilize some or all of the supplied N.
† Indicates in the Balance After Recs N column that the value includes residual N expected to become available that year from prior years’ manure
applications.

Appendix P: Sample Nutrient Management Plan
Section 6. Nutrient Management

P-19

NPDES Permit Writers’ Manual for CAFOs

6.9. Field Nutrient Status
Field Nutrient Status Details

Field
Details
(Please note that for ease of publication,
theNutrient
sample planStatus
provides
this information for Field 8 only.)
(Please note that for ease of publication, the sample plan provides this information for Field 8 only.)

Plan File: Sample
Operation: DEF Feedlot

Last Saved:
7/8/2010
Init. File Rev: 8/13/2009

State: Iowa

Year

Field ID

Sub ID

Nutrient Needs

Crop

2010
2010

Bob’s Farm North
Bob’s Farm North

8N
8N

Crop Fertilizer Recs
Crop Nutrient Removal

Soybean
Soybean

Date

Field ID

Sub ID

Nutrient Activity

Source

2010
2010
2010

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

Year

Field ID

Sub ID

Nutrient Needs

Crop

Yield Goal

2011
2011

Bob’s Farm North
Bob’s Farm North

8N
8N

Crop Fertilizer Recs
Crop Nutrient Removal

Corn
Corn

195 Bu
195 Bu

Date

Field ID

Sub ID

Nutrient Activity

Source

Equipment/Method

Rate

Acres

N

Nov 10
Nov 10
Apr 11

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Manure App (2-yr P)
Manure App (2-yr P)
Fertilizer App (1-yr N)

W SetdSolidBasin#4
E SetldSolidBasin #3
28-0-0

Dry Box Spreader
Dry Box Spreader
Shallow subsurface band(<4")

10.5 Ton
10.5 Ton
47 Gal

15.9
40.6
56.4

20
20
140

2011
2011
2011

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

56.4
56.4
56.4

Year

Field ID

Sub ID

Nutrient Needs

Crop

Yield Goal

2012
2012

Bob’s Farm North
Bob’s Farm North

8N
8N

Crop Fertilizer Recs
Crop Nutrient Removal

Soybean
Soybean

61 Bu
61 Bu

Date

Field ID

Sub ID

Nutrient Activity

Source

Rate

2012

Bob’s Farm North

8N

Residual Manure N

2012
2012
2012

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Total Nutrients Applied
Balance After Recs
Balance After Removal

Year

Field ID

Sub ID

Nutrient Needs

Crop

Yield Goal

2013
2013

Bob’s Farm North
Bob’s Farm North

8N
8N

Crop Fertilizer Recs
Crop Nutrient Removal

Corn
Corn

195 Bu
195 Bu

Date

Field ID

Sub ID

Nutrient Activity

Source

2013
May 13
Apr 13

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Residual Manure N
Manure App (1-yr P)
Fertilizer App (1-yr N)

E SetldSolidBasin #3
28-0-0

2013
2013
2013

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

Year

Field ID

Sub ID

Nutrient Needs

Crop

2014
2014

Bob’s Farm North
Bob’s Farm North

8N
8N

Crop Fertilizer Recs
Crop Nutrient Removal

Soybean
Soybean

Date

Field ID

Sub ID

Nutrient Activity

Source

2014
Apr 14
May 14

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Residual Manure N
Manure App (1-yr P)
Manure App (1-yr P)

E SetldSolidBasin #3
W SetdSolidBasin#4

2014
2014
2014

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

Year

Field ID

Sub ID

Nutrient Needs

Crop

2010
2010

Bob’s Farm South
Bob’s Farm South

8S
8S

Crop Fertilizer Recs
Crop Nutrient Removal

Soybean
Soybean

Date

Field ID

Sub ID

Nutrient Activity

Source

2010
2010
2010

Bob’s Farm South
Bob’s Farm South
Bob’s Farm South

8S
8S
8S

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

Year

Field ID

Sub ID

Nutrient Needs

Crop

2011
2011

Bob’s Farm South
Bob’s Farm South

8S
8S

Crop Fertilizer Recs
Crop Nutrient Removal

Corn
Corn

Equipment/Method

Equipment/Method

Yield Goal

Acres

N

61 Bu
61 Bu

56.4
56.4

0
232

P2O5

K2O

Rate

Acres

N

P2O5

K2O

56.4
56.4
56.4

0
0
-232

0
0
-49

0
0
-92

Acres

N

56.4
56.4

160

P2O5

K2O

P2O5

K2O

160
0

30
30
-43

92
92
33

Acres

N

56.4
56.4

0
232

P2O5

K2O

Acres

N

56.4

6

P2O5

K2O

56.4
56.4
56.4

6
0
-226

0
30
-49

0
92
-59

Acres

N

56.4
56.4

160

P2O5

K2O

Rate

Acres

N
3
35
122

P2O5

K2O

16 Ton
41 Gal

56.4
56.4
56.4

46
0

141
0

56.4
56.4
56.4

160
0

46
76
-27

141
233
82

Yield Goal

Acres

N

61 Bu
61 Bu

56.4
56.4

0
232

P2O5

K2O

Rate

Acres

N
10
37
37

P2O5

K2O

17 Ton
17 Ton

56.4
44.5
2.8

49
49

150
150

56.4
56.4
56.4

41
0ª
-191

41
117
-8

126
359
116

P2O5

K2O

Spreadable Area
Spreadable Area
Spreadable Area

Equipment/Method
Dry Box Spreader
Shallow subsurface band(<4")

Equipment/Method
Dry Box Spreader
Dry Box Spreader

Equipment/Method

0
49

0
73

30
30
0

0
49

0
73

0
49

0
92

0
59

92
92
0

0
92

0
59

0
92

Yield Goal

Acres

N

61 Bu
61 Bu

79.6
79.6

0
232

Rate

Acres

N

P2O5

K2O

79.6
79.6
79.6

0
0
-232

0
0
-49

0
0
-92

79.6
79.6

160

0
73

0
59

0
49

0
92

Appendix P: Sample Nutrient Management Plan
Yield Goal Acres
N P2O5
K2O
Section 6. Nutrient
Management
195 Bu
195 Bu

Date

Field ID

Sub ID

Nutrient Activity

2014
Apr 14
May 14

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Residual Manure N
Manure App (1-yr P)
Manure App (1-yr P)

E SetldSolidBasin #3
W SetdSolidBasin#4

2014
2014
2014

Bob’s Farm North
Bob’s Farm North
Bob’s Farm North

8N
8N
8N

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

Year

Field ID

Sub ID

Nutrient Needs

Crop

2010
2010

Bob’s Farm South
Bob’s Farm South

8S
8S

Crop Fertilizer Recs
Crop Nutrient Removal

Soybean
Soybean

Date

Field ID

Sub ID

Nutrient Activity

Source

2010
2010
2010

Bob’s Farm South
Bob’s Farm South
Bob’s Farm South

8S
8S
8S

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

Year

Field ID

Sub ID

Nutrient Needs

Crop

Yield Goal

2011
2011

Bob’s Farm South
Bob’s Farm South

8S
8S

Crop Fertilizer Recs
Crop Nutrient Removal

Corn
Corn

195 Bu
195 Bu

Date

Field ID

Sub ID

Nutrient Activity

Source

Equipment/Method

Rate

Acres

N

Nov 10
Apr 11

Bob’s Farm South
Bob’s Farm South

8S
8S

Manure App (3-yr P)
Fertilizer App (1-yr N)

E Lots Stack #1
28-0-0

Dry Box Spreader
Shallow subsurface band(<4")

19 Ton
43 Gal

79.7
79.6

32
128

2011
2011
2011

Bob’s Farm South
Bob’s Farm South
Bob’s Farm South

8S
8S
8S

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

79.6
79.6
79.6

Year

Field ID

Sub ID

Nutrient Needs

Crop

Yield Goal

2012
2012

Bob’s Farm South
Bob’s Farm South

8S
8S

Crop Fertilizer Recs
Crop Nutrient Removal

Soybean
Soybean

61 Bu
61 Bu

Date

Field ID

Sub ID

Nutrient Activity

Source

Rate

Acres

N

2012

Bob’s Farm South

8S

Residual Manure N

79.6

10

2012
2012
2012

Bob’s Farm South
Bob’s Farm South
Bob’s Farm South

8S
8S
8S

Total Nutrients Applied
Balance After Recs
Balance After Removal

79.6
79.6
79.6

Year

Field ID

Sub ID

Nutrient Needs

Crop

Yield Goal

2013
2013

Bob’s Farm South
Bob’s Farm South

8S
8S

Crop Fertilizer Recs
Crop Nutrient Removal

Corn
Corn

195 Bu
195 Bu

Date

Field ID

Sub ID

Nutrient Activity

Source

2013
Apr 13

Bob’s Farm South
Bob’s Farm South

8S
8S

Residual Manure N
Fertilizer App (1-yr N)

28-0-0

2013
2013
2013

Bob’s Farm South
Bob’s Farm South
Bob’s Farm South

8S
8S
8S

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

Year

Field ID

Sub ID

Nutrient Needs

Crop

2014
2014

Bob’s Farm South
Bob’s Farm South

8S
8S

Crop Fertilizer Recs
Crop Nutrient Removal

Soybean
Soybean

Date

Field ID

Sub ID

Nutrient Activity

Source

2014
2014
2014

Bob’s Farm South
Bob’s Farm South
Bob’s Farm South

8S
8S
8S

Total Nutrients Applied
Balance After Recs
Balance After Removal

Spreadable Area
Spreadable Area
Spreadable Area

P-20

Source

Equipment/Method
Dry Box Spreader
Dry Box Spreader

Rate

Acres

N

17 Ton
17 Ton

56.4
44.5
2.8

10
37
37

56.4
56.4
56.4

41
0ª
-191

K2O

49
49

150
150

41
117
-8

126
359
116

P2O5

K2O

NPDES Permit Writers’ Manual for CAFOs

Equipment/Method

Equipment/Method

Yield Goal

Acres

N

61 Bu
61 Bu

79.6
79.6

0
232

Rate

Acres

N

P2O5

K2O

79.6
79.6
79.6

0
0
-232

0
0
-49

0
0
-92

Acres

N

79.6
79.6

160

P2O5

K2O

P2O5

K2O

160
0

190
190
117

266
266
207

Acres

N

79.6
79.6

0
232

P2O5

K2O

P2O5

K2O

10
0
-222

0
190
68

0
266
115

Acres

N

79.6
79.6

160

P2O5

K2O

Rate

Acres

N
4
158

P2O5

K2O

53 Gal

79.6
79.6

0

0

79.6
79.6
79.6

162
2

0
190
-5

0
266
56

Yield Goal

Acres

N

61 Bu
61 Bu

79.6
79.6

0
232

P2O5

K2O

Rate

Acres

N

P2O5

K2O

79.6
79.6
79.6

0
0
-232

0
190
-49

0
266
-36

Spreadable Area
Spreadable Area
Spreadable Area

Equipment/Method
Shallow subsurface band(<4")

Equipment/Method

P2O5

0
49

0
73

190
0

0
49

0
73

0
49

Notes
(1) If a field has a non-spreadable area, it is listed in a separate section following the field's spreadable area.
(2) Yield Goal, Rate, N, P2O5 and K2O values are all per acre.
(3) The crop's N fertilizer rec accounts for any N credit from a previous legume crop.
(4) If a field has more than one manure application in the same crop year, or if the total area covered that year is less than or greater than the field's area, a field average
isused in calculating balances. This field average is the sum of each manure application's area times its per-acre amount of nutrient applied, divided by the field's area.
(5) Any positive P2O5 or K2O balance is carried over to the next year. Available N not utilized in the current crop year is assumed lost.
¤ Indicates a custom fertilizer recommendation in the Crop Fertilizer Recs columns.
ª Indicates in the Balance After Recs N column that the legume crop is assumed to utilize some or all of the supplied

Appendix P: Sample Nutrient Management Plan
Section 6. Nutrient Management

0
92

0
59

266
0

0
92

0
59

0
92

P-21

NPDES Permit Writers’ Manual for CAFOs

6.10. Manure Inventory Annual Summary
Manure Source
E Lots Stack #1

Plan Period
Oct '09–Sep '10

On Hand
at Start of
Period
200

Total
Generated
4,375

Total
Total
Total Trans­
Total Trans­
Im­ ferred
Ex­ ferred
In
Total Applied ported Out
ported
0

0

2,385

0

0

On Hand
at End of
Period

Units

2,190 Ton

E SetldSolidBasin #3

Oct '09–Sep '10

100

757

0

0

477

0

0

380 Ton

E Storage Pond #1

Oct '09–Sep '10

750,000

10,575,180

0

0

11,182,050

0

0

143,130 Gal

W Lots Stack #2

Oct '09–Sep '10

100

1,750

0

0

975

0

0

875 Ton

W SetdSolidBasin#4

Oct '09–Sep '10

75

247

0

0

195

0

0

127 Ton

W Storage Pond #2

Oct '09–Sep '10

400,000

5,876,413

0

0

5,182,199

0

0 1,094,214 Gal

All Sources (liquid) Oct '09–Sep '10 1,150,000 16,451,593

0

0 16,364,249

0

0 1,237,344 Gal

475

7,129

0

0

4,032

0

0

3,572 Ton

E Lots Stack #1

All Sources (solid) Oct '09–Sep '10
Oct '10–Sep '11

2,190

4,375

0

0

3,888

0

0

2,677 Ton

E SetldSolidBasin #3

Oct '10–Sep '11

380

757

0

0

678

0

0

459 Ton

E Storage Pond #1

Oct '10–Sep '11

143,130

10,575,180

0

0

10,165,500

0

0

552,810 Gal

W Lots Stack #2

Oct '10–Sep '11

875

1,750

0

0

1,752

0

0

873 Ton

W SetdSolidBasin#4

Oct '10–Sep '11

127

247

0

0

249

0

0

125 Ton

W Storage Pond #2

Oct '10–Sep '11

1,094,214

5,876,413

0

0

5,842,899

0

0

1,127,728 Gal

All Sources (liquid) Oct '10–Sep '11 1,237,344 16,451,593

0

0 16,008,399

0

0 1,680,538 Gal

3,572

7,129

0

0

6,567

0

0

4,134 Ton

E Lots Stack #1

All Sources (solid) Oct '10–Sep '11
Oct '11–Sep '12

2,677

4,375

0

0

4,157

0

0

2,896 Ton

E SetldSolidBasin #3

Oct '11–Sep '12

459

757

0

0

716

0

0

501 Ton

E Storage Pond #1

Oct '11–Sep '12

552,810

10,575,180

0

0

9,148,950

0

0 1,979,040 Gal

W Lots Stack #2

Oct '11–Sep '12

873

1,750

0

0

1,833

0

0

790 Ton

W SetdSolidBasin#4

Oct '11–Sep '12

125

247

0

0

144

0

0

228 Ton

W Storage Pond #2

Oct '11–Sep '12

1,127,728

5,876,413

0

0

5,842,899

0

0

1,161,242 Gal

All Sources (liquid) Oct '11–Sep '12 1,680,538 16,451,593

0

0 14,991,849

0

0 3,140,282 Gal

4,134

7,129

0

0

6,849

0

0

4,414 Ton

E Lots Stack #1

Oct '12–Sep '13

2,896

4,375

0

0

4,622

0

0

2,649 Ton

E SetldSolidBasin #3

Oct '12–Sep '13

501

757

0

0

903

0

0

355 Ton

All Sources (solid) Oct '11–Sep '12

E Storage Pond #1

Oct '12–Sep '13

1,979,040

10,575,180

0

0

10,165,500

0

0 2,388,720 Gal

W Lots Stack #2

Oct '12–Sep '13

790

1,750

0

0

1,332

0

0

1,208 Ton

W SetdSolidBasin#4

Oct '12–Sep '13

228

247

0

0

240

0

0

235 Ton

W Storage Pond #2

Oct '12–Sep '13

1,161,242

5,876,413

0

0

6,032,982

0

0 1,004,673 Gal

All Sources (liquid) Oct '12–Sep '13 3,140,282 16,451,593

0

0

16,198,482

0

0 3,393,393 Gal

0

0

7,097

0

0

4,447 Ton

All Sources (solid) Oct '12–Sep '13

4,414

7,129

E Lots Stack #1

Oct '13–Sep '14

2,649

4,375

0

0

2,714

0

0

4,311 Ton

E SetldSolidBasin #3

Oct '13–Sep '14

355

757

0

0

756

0

0

356 Ton

E Storage Pond #1

Oct '13–Sep '14

2,388,720

10,575,180

0

0

8,132,400

0

0 4,831,500 Gal

W Lots Stack #2

Oct '13–Sep '14

1,208

1,750

0

0

2,699

0

0

260 Ton

W SetdSolidBasin#4

Oct '13–Sep '14

235

247

0

0

273

0

0

209 Ton

W Storage Pond #2

Oct '13– Sep '14 1,004,673

5,876,413

0

0

6,881,019

0

0

67 Gal

All Sources (liquid) Oct '13–Sep '14 3,393,393 16,451,593

0

0

15,013,419

0

0 4,831,567 Gal

0

0

6,441

0

0

All Sources (solid) Oct '13–Sep '14

4,447

7,129

5,135 Ton

Appendix P: Sample Nutrient Management Plan
Section 6. Nutrient Management

P-22

NPDES Permit Writers’ Manual for CAFOs

6.11. Fertilizer Material Annual Summary
Product Analysis

Plan Period

Product
Needed
Oct–Dec

28-0-0

Oct '09–Sep '10

0

28-0-0

Oct '10–Sep '11

0

28-0-0

Oct '11–Sep '12

0

28-0-0

Oct '12–Sep '13

28-0-0

Oct '13–Sep '14

Product
Needed
Jan–Sep

Total Product
Needed

Units

54,461

54,461

Gal

46,909

46,909

Gal

51,098

51,098

Gal

0

43,833

43,833

Gal

0

59,803

59,803

Gal

6.12. Whole-farm Nutrient Balance (Manure-spreadable Area )
N (Lbs)
Total Manure Nutrients on Hand at Start of Plan

1

Total Manure Nutrients Collected

2

Total Manure Nutrients Imported3
Total Manure Nutrients Exported

4

Total Manure Nutrients on Hand at End of Plan5
Total Manure Nutrients Applied6

P2O5 (Lbs)

K 2O (Lbs)

5,438

4,082

9,190

393,872

361,937

719,700

0

0

0

0

0

0

44,663

49,753

83,442

354,897

317,506

646,223

Available Manure Nutrients Applied

118,283

317,506

646,223

Commercial Fertilizer Nutrients Applied8

763,771

0

0

Available Nutrients Applied

9

882,054

317,506

646,223

Nutrient Utilization Potential

1,243,599

409,494

422,760

-361,545

-91,988

223,463

-58

-15

36

7

10

Nutrient Balance of Spreadable Acres11*
Average Nutrient Balance per Spreadable Acre per Year12*
1.
2.
3.
4.
5.
6.
7.

Values indicate total manure nutrients present in storage(s) at the beginning of the plan.
Values indicate total manure nutrients collected on the farm.
Values indicate total manure nutrients imported onto the farm.
Values indicate total manure nutrients exported from the farm to an external operation.
Values indicate total manure nutrients present in storage(s) at the end of plan.
Values indicate total nutrients present in land-applied manure. Losses due to rate, timing and method of application are not included in these values.
Values indicate available manure nutrients applied on the farm based on rate, time and method of application. These values are based on the total
manure nutrients applied (row 6) after accounting for state-specific nutrient losses due to rate, time and method of application.
8. Values indicate nutrients applied as commercial fertilizers and nitrates contained in irrigation water.
9. Values are the sum of available manure nutrients applied (row 7) and commercial fertilizer nutrients applied (row 8).
10. Values indicate nutrient utilization potential of crops grown. For N the value generally is based on crop N recommendation for non-legume crops and
crop N uptake or other state-imposed limit for N application rates for legumes. P2O5 and K 2O values generally are based on fertilizer recommendations
or crop removal (whichever is greatest).
11. Values indicate available nutrients applied (row 9) minus crop nutrient utilization potential (row 10). Negative values indicate additional nutrient
utilization potential and positive values indicate over-application.
12. Values indicate average per acre nutrient balance. Values are calculated by dividing nutrient balance of spreadable acres (row 11) by the number of
spreadable acres in plan and by the length of the plan in years. Negative values indicate additional average per acre nutrient utilization potential and
positive values indicate average per acre over-application.
* Non-trivial, positive values for N indicate that the plan was not properly developed. Negative values for N indicate additional nutrient utilization potential
which may or may not be intentional. For example, plans that include legume crops often will not utilize the full N utilization potential for legume crops
if manure can be applied to non-legume crops that require N for optimum yield. Positive values for P2O5 and/or K 2O do not necessarily indicate that
the plan was not developed properly. For example, producers may be allowed to apply N-based application rates of manure to fields with low soil test
P values or fields with a low potential P-loss risk based on the risk assessment tool used by the state. Negative values for P2O5 and K 2O indicate that
planned applications to some fields are less than crop removal rates.

Appendix P: Sample Nutrient Management Plan
Section 6. Nutrient Management

P-23

NPDES Permit Writers’ Manual for CAFOs

Section 7. Record Keeping
7.1. Land Application Equipment Inspections
The equipment identified in the table below is used to apply manure, litter, and process wastewater. This
equipment will be inspected at least once annually, within one month before use. Inspection dates will be
recorded in the table below.
Inspection Date
Equipment

2010

2011

2012

2013

2014

Dry Box Spreader
Injector

7.2. Record Keeping Forms
The records identified below will be maintained at the indicated frequencies using the forms identified.
[Note: the referenced forms are included in Appendix D.]
Record
Visual inspections of structures used to store, contain,
or treat manure, litter, and process wastewater, including
wastewater levels as indicated on depth markers and
actions taken to correct deficiencies

Frequency

Form

Weekly

AFO Weekly Storage, Containment, and Treatment
Structure Inspections Log Sheet (a separate form
will be completed for each structure)

Visual inspections of storm water diversion structures and Weekly
channels including actions taken to correct deficiencies

CAFO Weekly Storm Water Diversion and Channel
Inspections Log Sheet

Per
application
event

CAFO Nutrient Land Application Log Sheet (a
separate form will be completed for each field)

Water line inspections, including drinking and cooling
water lines

Daily

Daily Water Line Inspection Log Sheet

Off-site transfers of manure, litter, and process
wastewater, including recipient name and address, date
of transfer, and amount transferred

Per transfer Manure, Litter, and Process Wastewater Transfer
event (if any) Record Form

Land application records, including
• Date of application
• Source of manure, litter, or process wastewater
applied
• Method of application
• Weather conditions during and for 24 hours before
and after application
• Amount of manure, litter, or process wastewater
applied
• Total N and P applied, including calculations

Appendix P: Sample Nutrient Management Plan
Section 7. Record Keeping

P-24

NPDES Permit Writers’ Manual for CAFOs

7.3. Records Maintained in NMP
In addition, the following records will be maintained as indicated below.
Record

Frequency

Documentation Method/Location

Expected crop yield

Once per permit/ NMP Section 6.5
NMP cycle
unless NMP
revised

Test methods used to sample and analyze manure,
litter, soil, and process wastewater

Per sampling
event

Methods identified on laboratory reports

Results from manure, litter, process wastewater, and
soil sampling

Per sampling
event

Laboratory reports of analytical results maintained
with NMP

Basis for determining manure application rates in
accordance with the technical standards for nutrient
management identified in the permit

Once per permit/ NMP outlines basis for rate determination
NMP cycle
unless NMP
revised

Calculations showing the total amount of N and P to
be applied to each field

Once per permit/ Calculations are performed within MMP software;
NMP cycle
data inputs and results are included in NMP
unless NMP
revised

Appendix P: Sample Nutrient Management Plan
Section 7. Record Keeping

P-25

NPDES Permit Writers’ Manual for CAFOs

Section 8. Publications and References
8.1. Publications
Crop Fertilizer Recommendations
“Crop Nutrient Recommendations,” PM 1688, Sept 2008
http://www.extension.iastate.edu/Publications/PM1688.pdf

Manure Nutrient Availability
“Managing Manure Nutrients for Crop Production,” Iowa State Extension, PM 1811, Nov. 2003
This document no longer exists on Iowa State Extension’s web site. Similar technical information
can be found in “Using Manure Nutrients for Crop Production,” Iowa State Extension, PMR 1003,
September 2008.
http://www.extension.iastate.edu/Publications/PMR1003.pdf

Phosphorus Assessment
“Technical Note No. 25, Iowa Phosphorus Index,” Iowa NRCS, August 2004
ftp://ftp-fc.sc.egov.usda.gov/IA/technical/Technot25Aug04.pdf

Practice Standards
Iowa NRCS Nutrient Management Standard (590), December 2008
http://efotg.sc.egov.usda.gov//references/public/IA/IA590Dec08.pdf

8.2. Software and Data Sources
MMP Version

MMP 0.2.9.0

MMP Plan File

Sample

MMP Initialization File for Iowa

8/13/2009

MMP Soils File for Iowa

11/17/2009

Phosphorus Assessment Tool

2007.06.29

NRCS Conservation Plan(s)

n/a

RUSLE2 Library

Version: 1.32.3.0
Build: Dec 17 2007
Science: 20061020

RUSLE2 Database

moses1.gdb

Appendix P: Sample Nutrient Management Plan
Section 8. Publications and References

P-26

NPDES Permit Writers’ Manual for CAFOs

8.3. Initialization Files
Initialization File Summary
Init. File: ia.mmi

State: Iowa

Revision: 8/13/2009

Crops
N
P 2O5
K 2O
Removed Removed Removed

Name

Yield
Units

Alfalfa hay

Ton

50

12.5

40.0

"Crop Nutrient Recommendations," PM 1688, Sept 2008

Alfalfa seeding

Ton

50

12.5

40.0

"Crop Nutrient Recommendations," PM 1688, Sept 2008

Alfalfa-grass hay

Ton

50

12.5

40.0

"Crop Nutrient Recommendations," PM 1688, Sept 2008

Alfalfa-grass pasture

Ton

50

8.3

20.0

"Crop Nutrient Recommendations," PM 1688, Sept 2008

Bluegrass pasture

Ton

9

30

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Bromegrass hay

Ton

40

9

47

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Bromegrass pasture

Ton

40

6

23.5

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Clover/trefoil-grass
hay

Ton

43

12

35

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Clover/trefoil-grass
past

Ton

43

8

17.5

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Corn

Bu

0.375

0.30

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Managing Manure Nutrients," PM 1811, Nov 03

Corn silage

Ton

3.5

8

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Managing Manure Nutrients," PM 1811, Nov 03

(Lb/YldUnit) (Lb/YldUnit) (Lb/YldUnit)

Source of Fertilizer Recommendations

CRP
Fallow
Legume cover
Oat

Bu

0.75

0.4

1.0

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Managing Manure Nutrients," PM 1811, Nov 03

Oat + forage
seeding

Bu

0.75

0.4

1.0

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Managing Manure Nutrients," PM 1811, Nov 03

Orchardgrass hay

Ton

38

14

68

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Orchardgrass
pasture

Ton

38

9.3

34

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Perennial ryegrass
hay

Ton

24

12

34

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Perennial ryegrass
past

Ton

24

8

17

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Reed canarygrass
hay

Ton

9

47

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Reed canarygrass
pasture

Ton

6

23.5

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Other

Appendix P: Sample Nutrient Management Plan
Section 8. Publications and References

P-27

NPDES Permit Writers’ Manual for CAFOs

Initialization File Summary
Init. File: ia.mmi
Name

State: Iowa
Yield
Units

N
P 2O5
K 2O
Removed Removed Removed

Revision: 8/13/2009
Source of Fertilizer Recommendations

(Lb/YldUnit) (Lb/YldUnit) (Lb/YldUnit)

Small grain cover
Sorg-sudan hay

Ton

40

12

38

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Sorg-sudan pasture

Ton

40

8

19

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Soybean

Bu

3.8

0.8

1.5

"Crop Nutrient Recommendations," PM 1688, Sept 2008

Sunflower

CWT

3.5

0.8

0.7

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Managing Manure Nutrients," PM 1811, Nov 03

Switchgrass hay

Ton

21

12

66

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Switchgrass pasture

Ton

21

8

33

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Tall fescue hay

Ton

38

12

66

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Tall fescue pasture

Ton

38

8

33

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Timothy hay

Ton

25

9

32

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Timothy pasture

Ton

25

6

16

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Fertilizing Pasture," PM 869, June 1997

Wheat

Bu

1.3

0.6

0.3

"Crop Nutrient Recommendations," PM 1688, Sept 2008 and
"Managing Manure Nutrients," PM 1811, Nov 03

Initialization File Summary
Init. File: ia.mmi

State: Iowa

Revision: 8/13/2009

Storage Types
Name

% N Lost in % Org. N
Handling & Mineralized
Storage
First Year

Water
Dilution
Factor

Source of Storage N Data

Manure pack

30

25

1

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Open lot

50

35

1

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Dry stack

25

45

1

Adapted from "Livestock Waste Facilities Handbook,"
MWPS-18, Third Edition, 1993

Underfloor dry
storage

35

60

1

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Litter

35

60

1

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Daily scrape & haul
(liquid)

25

25

1

Adapted from "Livestock Waste Facilities Handbook,"
MWPS-18, Third Edition, 1993

Underfloor liquid
storage

20

35

1

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Appendix P: Sample Nutrient Management Plan
Section 8. Publications and References

P-28

NPDES Permit Writers’ Manual for CAFOs

Initialization File Summary
Init. File: ia.mmi
Name

State: Iowa
% N Lost in % Org. N
Handling & Mineralized
Storage
First Year

Revision: 8/13/2009

Water
Dilution
Factor

Source of Storage N Data

Outside prefab liquid
storage

20

30

1.2

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Earthen storage

30

30

1.4

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Lagoon, 1 stage

75

30

2.5

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Lagoon, 2 stage

80

30

2.5

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Lagoon, 3 stage

80

30

2.5

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Washwater

75

30

6

"Livestock Waste Facilities Handbook," MWPS-18,
Third Edition, 1993

Initialization File Summary
Init. File: ia.mmi

State: Iowa

Revision: 8/13/2009

Animal Types
Name

Daily
Daily
Daily
Manure Manure Total N
(Lb/AU) (Gal/AU) (Lb/AU)

Daily
P 2 O5
(Lb/AU)

Daily
Water
K 2O
Dilution
(Lb/AU) Factor

Source of Daily Excretion Data

Sow & litter

59

7.3

0.45

0.30

0.34

1.4

AWMFH Chapter 4, Table 4-10(c),
March 2008

Nursery pig

88

10.5

0.92

0.34

0.42

1.5

AWMFH Chapter 4, Table 4-10(d),
March 2008

Grow-finish pig

65

8.2

0.54

0.21

0.29

1.25

AWMFH Chapter 4, Table 4-10(d),
March 2008

Wean-to-finish pig

71

8.8

0.64

0.23

0.32

1.3

AWMFH Chapter 4, Table 4-10(d),
March 2008

Gestating sow

25

3.1

0.16

0.11

0.13

1.3

AWMFH Chapter 4, Table 4-10(c),
March 2008

Boar

19

2.2

0.14

0.11

0.11

1.2

AWMFH Chapter 4, Table 4-10(c),
March 2008

Calf (dairy)

83

9.7

0.42

0.11

0.13

1.05

AWMFH Chapter 4, Table 4-5(b),
March 2008

Weaned heifer/steer
(dairy)

56

6.7

0.27

0.11

0.14

1.05

AWMFH Chapter 4, Table 4-5(b),
March 2008

Growing heifer/steer
(dairy)

56

6.7

0.27

0.11

0.14

1.05

AWMFH Chapter 4, Table 4-5(b),
March 2008

Breeding heifer
(dairy)

56

6.7

0.27

0.11

0.14

1.05

AWMFH Chapter 4, Table 4-5(b),
March 2008

Milk cow (dairy)

108

12.7

0.71

0.27

0.40

1.05

AWMFH Chapter 4, Table 4-5(b),
March 2008

Dry cow (dairy)

51

6.3

0.30

0.10

0.12

1.05

AWMFH Chapter 4, Table 4-5(b),
March 2008

Appendix P: Sample Nutrient Management Plan
Section 8. Publications and References

P-29

NPDES Permit Writers’ Manual for CAFOs

Initialization File Summary
Init. File: ia.mmi
Name

State: Iowa
Daily
Daily
Daily
Manure Manure Total N
(Lb/AU) (Gal/AU) (Lb/AU)

Daily
P 2 O5
(Lb/AU)

Revision: 8/13/2009

Daily
Water
K 2O
Dilution
(Lb/AU) Factor

SSource of Daily Excretion Data

Veal calf

60

7.2

0.20

0.07

0.30

1.05

AWMFH Chapter 4, Table 4-12,
March 2008

Suckling calf (beef)

77

9.0

0.45

0.18

0.35

1.05

AWMFH Chapter 4, Table 4-8(b),
March 2008

Weaned calf (beef)

77

9.0

0.45

0.18

0.35

1.05

AWMFH Chapter 4, Table 4-8(b),
March 2008

Growing steer (beef)

77

9.0

0.45

0.18

0.35

1.05

AWMFH Chapter 4, Table 4-8(b),
March 2008

Finishing steer
(beef)

65

8.2

0.36

0.10

0.30

1.05

AWMFH Chapter 4, Table 4-8(d),
March 2008

104

12.7

0.35

0.18

0.30

1.05

AWMFH Chapter 4, Table 4-8(b),
March 2008

Sheep

40

4.7

0.45

0.16

0.36

1.0

AWMFH Chapter 4, Table 4-13,
March 2008

Horse

51

6.1

0.18

0.06

0.06

1.0

AWMFH Chapter 4, Table 4-14(b),
March 2008

Broiler

88

10.5

0.96

0.64

0.65

1.0

AWMFH Chapter 4, Table 4-11(d),
March 2008

Layer

57

7.0

1.10

0.76

0.47

1.0

AWMFH Chapter 4, Table 4-11(b),
March 2008

Turkey tom

34

4.3

0.53

0.37

0.30

1.0

AWMFH Chapter 4, Table 4-11(d),
March 2008

Turkey hen

48

5.8

0.72

0.46

0.37

1.0

AWMFH Chapter 4, Table 4-11(d),
March 2008

102

12.7

1.00

0.80

0.60

1.0

AWMFH Chapter 4, Table 4-11(d),
March 2008

Brood cow/heifer
(beef)

Duck

Initialization File Summary
Init. File: ia.mmi

State: Iowa

Revision: 8/13/2009

Ration Amendments
Name
Wet/Dry Feeding
Phased Feeding
Phytase

Water Dilution
% Reduced

Total N
Production
% Reduced

P2O5 Production
% Reduced

K 2O Production
% Reduced

10

10

10

Storage N Loss
% Reduced

50

20

Alum

25

HAP Corn

20

HAP Soybean

20

Appendix P: Sample Nutrient Management Plan
Section 8. Publications and References

P-30

NPDES Permit Writers’ Manual for CAFOs

Initialization File Summary
Init. File: ia.mmi

State: Iowa

Revision: 8/13/2009

Equipment Types
Name

Is Liquid

Is Injected

Is Irrigated

Has Aerial N
Loss

Capacity
Units

Application
Units

Ton

Feet

Gal

Feet

Gal

Feet

Gal

Feet

Gal/Min

Feet

Gal/Min

Feet

Solid spreader



Liquid spreader, injected



Liquid spreader, surface spray



Liquid spreader, knives up



Hose pull, injected



Hose pull, knives up



Traveling gun







Gal/Min

Feet

Standing pipe







Gal/Min

Acres

Center pivot







Gal/Min

Acres






Initialization File Summary
Init. File: ia.mmi

State: Iowa

Revision: 8/13/2009

Misc.
% Total P Manure Available

100

% Total K Manure Available

100

CEC Estimation

K/390 + Ca/200 + Mg/120 + 12*(7 - Min(BufferpH, 7))

Soil Test P Change

Round(NetP2O5/20)

Soil Test K Change

Round((NetK2O - NumYears*20) / (4 + 0.2*CEC))

Source of Manure N Availability Data

“Managing Manure Nutrients for Crop Production,” Iowa State
Extension, PM 1811, Nov. 2003

Appendix P: Sample Nutrient Management Plan
Section 8. Publications and References