National Pollutant Discharge Elimination System (NPDES)

Animal Feeding Operations (AFOs) - Permitting Program

NPDES Permitting of CAFOs

Most states are authorized to issue NPDES permits. The operator of a concentrated animal feeding operation (CAFO) in an authorized state should request coverage from the appropriate state agency and utilize the appropriate state forms. See AFO State Contacts 

EPA is the permitting authority in Idaho, Massachusetts, New Hampshire, New Mexico, the District of Columbia, tribal lands, and U.S. territories. CAFO operators in these jurisdictions should contact the appropriate EPA contact and use the following EPA forms to request permit coverage. See AFO EPA Headquarters or Regional Contacts 

Annual NPDES CAFO Program Status Reports

EPA compiles annual summaries on the implementation status of the NPDES CAFO regulations. Reports include, for each state: total number of CAFOs, number and percentage of CAFOs with NPDES permits, and other information associated with implementation of the 2008 CAFO rule.



Regulatory Flexibility Act Section 610 Review of the National Pollutant Discharge Elimination System (NPDES) Permit Regulation and Effluent Limitations Guidelines and Standards for Concentrated Animal Feeding Operations (CAFOs) - Review of the 2003 NPDES permit regulation and effluent limitations guidelines (ELG) standards for CAFOs pursuant to section 610 of the Regulatory Flexibility Act (RFA).


EPA Administered Permit Programs: The National Pollutant Discharge Elimination System - This document consolidates the current federal CAFO regulatory requirements included in the 2012 CAFO rule revision to remove the Fifth Circuit Court’s vacated elements, and the 2008 and 2003 final CAFO rules into a single document.

National Pollutant Discharge Elimination System (NPDES) Concentrated Animal Feeding Operation (CAFO) Reporting Rule EPA co-proposed two options for obtaining basic information from CAFOs to support EPA in meeting its water quality protection responsibilities under the Clean Water Act (CWA). EPA withdrew the proposed rule in 2012. 


Revised National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitations Guidelines for Concentrated Animal Feeding Operations - EPA revised provisions of the 2008 CAFO rule that the Fifth Circuit Court of Appeals had vacated; in particular clarifying that CAFOs are required to have permits when they discharge as opposed to when they propose to discharge.


Revised National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitations Guidelines for Concentrated Animal Feeding Operations in Response to the Waterkeeper Decision This final rule furthers the statutory goal of restoring and maintaining the nation’s water quality by ensuring that CAFOs properly manage manure generated by their operations.


National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitation Guidelines and Standards for Concentrated Animal Feeding Operations (CAFOs) - Revises and clarifies the EPA's regulatory requirements for CAFOs under the CWA. This final rule ensures that CAFOs take appropriate actions to manage manure effectively in order to protect the nation's water quality. The rule revises two sections of the Code of Federal Regulations (CFR), the NPDES permitting requirements for CAFOs (Sec. 122), and ELGs for CAFOs (Sec. 412).


NPDES Permit Writers' Manual for Concentrated Animal Feeding Operations (CAFOs) - Provides information to states, producers, and the general public including:

  • general information on Clean Water Act (CWA) and NPDES requirements for CAFOs,
  • information to explain CAFO permitting requirements under the CWA, and
  • technical information to help states and producers understand options for nutrient management planning.

Implementation Guidance on CAFO Regulations – CAFOs That Discharge or Are Proposing to Discharge - Provides information, consistent with the 2008 CAFO rule, on complying with the requirement to obtain permit coverage if the CAFO discharges or proposes to discharge.
NOTE: This document has not been updated to address EPA’s 2012 regulatory revision (77 FR 65840) (October 31, 2012).

Managing Manure Nutrients at CAFOs - Provides additional technical information for owners, operators, technical service providers, consultants, and permit authorities on how to carry out EPA's 2003 regulatory requirements for NPDES permitting of CAFOs. It also provides information on voluntary technologies and management practices that may both improve the production efficiency of CAFOs and further protect the quality of the nation's waters.
NOTE: This document has not been updated to reflect the 2008 revisions to the final CAFO regulations. Portions of this document describing rule provisions that were not revised in 2008 are still relevant.

The Compendium of State Approaches for Manure Management

This compendium showcases examples of state programs for promoting good manure management at animal feeding operations. The examples are noteworthy because they show clear evidence of on-the-ground implementation and focus on meaningful environmental outcomes. 


Throughout history, people who raise livestock and poultry have used manure as a fertilizer, soil amendment, energy source, and even construction material. Today, farmers and ranchers manage tons of animal manure on 1.3 million farms and ranches in the United States. When manure is properly managed, stored, and utilized to maximize its value and minimize its pollution potential, the environment, farmers and ranchers benefit (see Beneficial Uses of Manure and Environmental Protection).

When excess nutrients, pathogens, organic matter and solids from manure discharge to surface waters they can cause excess algae growth and deplete the water of oxygen needed by fish and other aquatic life; they can also make the water unsafe for recreational activities and as a source of drinking water. Manure pollutants can also leach through the soil and enter the groundwater, making it unsafe for drinking.

The Clean Water Act NPDES Concentrated Animal Feeding Operation (CAFO) program provides a federal foundation for regulating discharges from some animal feeding operations. However, the widest array of programs, policies and tools originate with state programs, and include: variations on the federal NPDES program; state regulatory programs and voluntary programs. This compendium focuses on elements of state programs, ranging from specialized tools and training to state-specific regulations and permitting.

The Compendium

This compendium provides examples of state programs for promoting good manure management at animal feeding operations. The examples are noteworthy because they show clear evidence of on-the-ground implementation and focus on meaningful environmental outcomes.

The write-ups for each of the manure management programs in the compendium include:

  • An overview of the state program feature (e.g., state permit provision, program component, tool, or guidance relating to manure management)
  • Excerpts of state permit or regulatory language, as relevant
  • Information on which operations are covered under the state effort
  • Background on state frameworks and resources that serve as the basis for the program feature
  • Information on on-the-ground implementation, including the level of participation
  • Results of implementation
  • References to key state resources

EPA does not consider this list to be exhaustive and may add additional case studies to the compendium as they are identified and developed.

The inclusion of any particular state program feature for manure management should not be read as an EPA endorsement of the state program for AFOs as a whole. The compendium also should not be construed as a rating or ranking of any kind. In addition, this document does not impose any new legally binding requirements on EPA, states, or the regulated community. EPA has made every attempt to ensure the accuracy of the examples included in this document, and provided states with the opportunity to review and comment on the write-ups. If a conflict exists between this compendium and any statute, regulation, or permit, the statute, regulation or permit is the final authority.

Permits and Regulatory Programs

Part A of the compendium provides examples of program features for manure management that have a regulatory basis, such as permit provisions and other regulatory program elements. The examples include program features such as manure transfer requirements, facility registration requirements, and nutrient management inspector qualifications. Some examples are"" components of the state’s NPDES program, others are based on state-specific non-NPDES requirements. Each example is identifiable as such by the symbols shown at the right.

  • California: Implementing TMDL Wasteload Allocations
  • Michigan: Manure Transfer Requirements
  • Minnesota: Feedlot Registration
  • Nevada: CAFO Drainage Collection Requirements
  • Oregon: Plan Review and Public Notice of Substantial Changes
  • Virginia: Nutrient Management Inspector Qualifications

Non-Regulatory Tools, Guidance, and Support

Part B includes examples of non-regulatory tools, guidance, or other program features related to manure management. These examples include program features such as manure relocation programs, manure spreading advisory tools, and operator training.

  • Delaware: Manure Relocation Program
  • Delaware: Nutrient Management Planning Assistance
  • Oregon: Manure Spreading Advisory Tool
  • Oregon: Recordkeeping Calendar and Online Database
  • South Dakota: Environmental Training Program for Livestock Producers

Integrated Approaches

Part C of the compendium describes state regulatory features that integrate approaches across environmental media.These approaches address surface water quality impacts from manure management and environmental impacts in other areas such as air quality, groundwater, or emergency response. Although these program features are outside the scope of the CWA, they are included because they illustrate effective approaches to integrating environmental protection in a single regulatory tool, thereby simplifying requirements for farmers and ranchers.

  • California: Lagoon Construction Standards
  • California: Groundwater Protection
  • Minnesota: Air Emissions Plan
  • New Mexico: Groundwater Protection


The purpose of this document is to share some transferable examples of state programs that are successful in promoting good manure management at animal feeding operations. The state examples that are included are implemented on the ground, and are focused on achieving environmental benefits.This is meant to be a living document which EPA intends to add additional case studies to in the future. Suggestions for additional case studies can be sent to



Regulatory Definitions of Large CAFOs, Medium CAFOs, and Small CAFOs  - This factsheet defines a large, medium, and small concentrated animal feeding operation (CAFO).


Unified National Strategy for Animal Feeding Operations - Document sets forth a framework of actions, for the U.S. Department of Agriculture (USDA) and EPA under existing legal and regulatory authority, to reduce impacts to water quality and public health from improperly managed animal wastes.


Policy Statement on Scope of Discharge Authorization and Shield Associated with NPDES Permits (July 1, 1994) - EPA's position on the scope of the authorization to discharge under an NPDES permit and the shield thus associated with the permit authorization.