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National Pollutant Discharge Elimination System (NPDES)

Animal Feeding Operations (AFOs)


Animal Feeding Operations (AFOs) are agricultural operations where animals are kept and raised in confined situations. An AFO is 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.

AFOs that meet the regulatory definition of a concentrated animal feeding operation (CAFO) are regulated under the NPDES permitting program. The NPDES program regulates the discharge of pollutants from point sources to waters of the United States. CAFOs are point sources, as defined by the CWA [Section 502(14)] (PDF)(3 pp, 132 KB, About PDF). To be considered a CAFO, a facility must first be defined as an AFO, and meet the criteria established in the CAFO regulation.

AFOs and Environmental Considerations

Manure and wastewater from AFOs have the potential to contribute pollutants such as nitrogen and phosphorus, organic matter, sediments, pathogens, hormones, and antibiotics to the environment.

For detailed information on environmental considerations associated with animal agriculture, see:

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Links to Other Resources

EPA Agriculture Resource Directory - EPA’s National Agriculture Center compiles agriculture-related information from across EPA.

Farm, Ranch, and Rural Communities Federal Advisory Committee (FRRCC) - EPA established the FRCCC in 2008 to provide independent policy advice, information, and recommendations to the EPA Administrator on a range of environmental issues and policies that are important to agriculture and rural communities.

Agriculture: Climate Change - Information on climate change related to agriculture.

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NPDES CAFO Permitting

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 of CAFOs with NPDES permits, and other information associated with implementation of the CAFO regulations.

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Regulations and Guidance



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. 

National Pollutant Discharge Elimination System Permit Regulation for Concentrated Animal Feeding Operations: Removal of Vacated Elements in Response to 2011 Court Decision - 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).

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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.

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

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Compendium of State Approaches for Manure Management

This compendium showcases examples of state program features 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

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.

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.

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.


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 the CAFO Team (

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Outreach and Education

EPA has worked with the U.S. Department of Agriculture Natural Resources Conservation Service and the Animal Agriculture Discussion Group to develop education, outreach, and training materials to facilitate improved understanding of livestock and poultry feeding operations and water quality protection measures.

Open Dialogue

EPA established an Animal Agriculture Discussion Group (AADG) to develop a shared understanding of how to implement the Clean Water Act. AADG keeps communication open and improves two-way understandings of viewpoints. AADG is an informal and iterative group of animal agriculture stakeholders including representatives from the U.S. Department of Agriculture, all sectors of the animal feeding industry and their associations, academia, and states. The group convenes via conference calls and face-to-face meetings twice per year.

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Uses of Manure

Throughout history, people who raise livestock and poultry have used manure as a fertilizer, soil amendment, energy source, even construction material. Manure contains many useful, recyclable components, including nutrients, organic matter, solids, energy, and fiber. With today’s technology, manure can be used more efficiently and in more ways than ever, which should mitigate many of the environmental impacts that result when manure is treated as a waste.

Diagram of sources and components of animal manure


Farmers, gardeners, landscapers, and others commonly use livestock manure as a fertilizer to provide nutrients needed for crop production. Manure nutrients have real value as fertilizer. Manure’s fertilizer value will increase as the price of commercial fertilizers increase.

Like commercial fertilizer, manure must be managed properly to avoid environmental impacts. Manure has fertilizer value in its raw form; however, processing manure through digestion, composting, or other means can yield materials that are more portable and whose nutrients are more available to plants, more balanced to crop needs, or less prone to environmental losses.

Fresh ManureApplying fresh manure to farmland

Using fresh manure as a fertilizer to raise crops that will be fed back to the livestock, either directly or as a by-product of further processing, is an excellent way to recycle nutrients. Ideally, fresh manure would be used on the farm where the manure is generated or on a neighboring farm, because fresh manure is expensive to haul even short distances.

Livestock manure is commonly land-applied as a semi-solid or liquid. Farmers can incorporate manure into the soil or inject it under the soil surface to reduce the risk of runoff losses and odor problems. Sometimes manure solids are separated from the liquid. Following liquid/solid manure separation, the remaining manure liquids still contain about half of the original nutrients. The solids can be used for bedding or for other uses and the liquids can be land applied to both water and fertilize crops.

Farmers are the most common users of fresh manure for fertilizer, but home gardeners and landscapers also sometimes fertilize with fresh manure.

CompostApplying compost to farmland

Composting livestock manure reduces odors, kills disease-causing agents (pathogens), reduces bulk, and stabilizes the manure for easier handling. A properly constructed and managed manure composting operation can also process mortalities Exit(dead animals) from livestock operations. In some parts of the country, composting operations must be intensively managed to guarantee pathogen-free compost that meets requirements of both health regulations and public perception.

Compost can be applied more evenly and with better control than manure. The nitrogen in compost is not as readily available to plants as the nitrogen in fresh manure, but the availability of phosphorus, potassium and other nutrients from compost is similar to, or higher than, the availability of those nutrients from fresh manure.

Farmers and ranchers can use composted manure at their own operations as fertilizer or bedding. Sales of compost can remove excess nutrients from farms and ranches that cannot use all of their manure nutrients for their own needs.

Compost is less expensive to transport than fresh manure due to its lower moisture content, and more profitable to transport because of its higher market value. This means that compost has more potential for use in areas farther from the farm. Manure compost can be used for many purposes in non-agricultural areas, including site restoration, erosion control, soil remediation, and wetland restoration.

Compost users include gardeners, landscapers, vegetable farmers, turf growers, golf course managers, ornamental crop growers, and homeowners. More information about manure composting is available from numerous sources, for example: 

Other Manure ProductsPelletized manure

Pelletizing compacts fresh manure at high temperature and pressure to convert it into a dry finished product. Pellets are useful as a soil amendment or fertilizer. Because the pellets take up a smaller volume, they can be more easily stored and transported than manure. In some cases, processing can result in a product with a consistent and predictable nutrient content, making it more convenient for crop production and other uses. The pelletizing process is mainly used for poultry litter but could be applied to separated solids from other manures.

Nutrient extraction technologies, or manure nutrient recovery technologies, can remove nutrients from manure for fertilizer products. Nutrient extraction removes elemental nutrients from raw manure, separated liquids, or residuals of anaerobic digestion by chemical precipitation or coagulation. Examples of fertilizer products that can be generated with nutrient extraction systems are ammonium sulfate, calcium phosphate, and magnesium ammonium sulfate (struvite) crystals.

Biomass Conversion

Bioconversion involves growing organisms on manure or manure nutrients and then harvesting them to use as components of animal feed, fertilizer, or soil amendments.

Algae grown on nutrients from dairy wastewater can be harvested to produce a product used in plant fertilizersAlgae grown on nutrients from dairy wastewater and high-protein animal feed supplements. Black soldier fly larvae eat manure, killing disease-causing agents (pathogens) and transferring the manure nutrients to their bodies. The nutrient-rich larvae are a value-added product that can be exported off the farm. High protein feeds made with products like these can be worth up to $500 per ton. The manure left over after the larvae are harvested is useful as a soil amendment or fertilizer similar to compost.

Vermicomposting uses worms to digest manure, creating pathogen-free, nutrient-rich products that can be sold and Vermicomposting worms to digest manureexported off the farm. Worms produce nutrient-rich castings. The castings, along with the manure used to grow the worms, are useful as a fertilizer or soil amendment. This vermicompost is said to contain more available plant nutrients than conventional compost. In addition to the revenue from selling the vermicompost, the worms can be sold as fishing bait or processed for supplemental feed for poultry or fish operations.

Organic MatterApplying organic matter to farmland

Farmers, gardeners, and others use livestock manure as a soil amendment to improve soil quality. In addition to providing nutrients for plant growth, applying fresh or composted livestock manure to cropland improves soil organic matter and tilth (the physical conditions that make a soil suitable for growing crops). Applying livestock manure to cropland increases the amount of organic matter in the soil which improves the soil structure and can increase the soil’s ability to hold water.

Increasing soil organic matter also helps keep carbon in the soil (“carbon sequestration”) and out of the atmosphere where it can form the greenhouse gas carbon dioxide. Manure provides these benefits when it is applied in raw form or when solids are applied after solid-liquid separation, pelletizing, digestion, or composting.

Biochar is a charcoal carbon produced by burning biomass (including manure) in a low-oxygen environment.Biochar used to enhance soils and store carbon Biochar can enhance soils and store carbon. When used as a soil amendment, biochar provides nutrients in a stable form that is available to plants, reducing the risk of runoff losses or leaching to groundwater. Biochar also improves soil tilth, porosity, water holding capacity, cation exchange capacity (CEC), soil biology, and fertilizer efficiency. Biochar is a stable form of soil organic carbon, sequestering carbon for potentially thousands of years.

SolidsUsing manure solids for animal bedding

Some dairy farms use sawdust, wood shavings, straw, sand, or other purchased materials as animal bedding. Bedding can be expensive—on the order of $40 to $50/cow/year. In recent decades, traditional bedding materials like sawdust or sand have become more expensive. Solid material can be recovered from manure (through solid-liquid separation, composting, or anaerobic digestion) and used as bedding, replacing materials purchased from off the farm.

Dried manure solids can be used for bedding without adversely affecting herd health.


Livestock manure can be processed to produce fuels for heating, transportation, and energy generation. These fuels can be used on the farm to replace purchased fuel or can be sold off the farm. In some cases, manure can be burned to generate electricity. However, processing manure for intermediate energy products like biogas, bio-oil, and syngas is much more common.

BiogasBiogas recovered from anaerobic digesters used for generating heat or electricity

Biogas recovered from anaerobic digesters is useful for generating heat or electricity to use on the farm or sell to the local power grid. Biogas production usually uses dairy or swine manure because of their relatively high methane producing potential. However, some digesters in the U.S. use beef manure or poultry litter as feedstocks.

Gas from anaerobic digestion is about 60 to 80 percent methane and has a heating value of 600 – 800 BTU/ft3. (As a comparison, natural gas generally contains more than 85 percent methane and has a heating value of about 950 – 1050 BTU/ft3). Most equipment that uses natural gas, butane, or propane as fuel can be modified to use biogas. This includes boilers, space heaters, and electrical generators.

Because digesters capture methane and other air pollutants, they reduce harmful air emissions from manure and provide superior odor control. Using biogas from digesters also offsets fuel consumption and emissions from non-renewable fossil fuels.

Anaerobic digestion to produce biogas (as well as other types of energy products and technologies) usually needs to operate on a large scale to be economically feasible. Anaerobic digestion can be technically complex and can be too expensive, especially for small operations. The process can be more affordable if manure is co-digested with off-farm wastes (such as green waste and food waste).

Bio-oilLiquid bio-oil fuels produced from manure

Liquid bio-oil fuels can be produced from manure by thermochemical processes like pyrolysis and gasification. Bioconversion, such as growing algae with manure nutrients, is another process that can produce bio-oil.

Bio-oils are physically different from petroleum-based fuel oil. For example, bio-oils have a lower energy content per gallon and higher acidity than petroleum-based fuel oil. However, tests indicate that bio-oil could be used for applications such as heating or generating electricity.

Commercial experience with biodiesel has been very promising. Biodiesel performs as well as petroleum diesel, while reducing air emissions of particulate matter, carbon monoxide, hydrocarbons and sulfur oxides. 

Most production of biodiesel from thermochemical processes involves poultry litter because it is already dry and does not require additional energy inputs for drying wet manure.
The technology may be used for other types of manure in areas of the country where manure is commonly air-dried.


Gasification can covert manure (at present mainly poultry litter) into a synthetic gas fuel composed of a mixture of water vapor, tars, hydrogen gas, carbon monoxide, carbon dioxide, nitrogen gas, and hydrocarbon gases. Some of the gas condenses to form a combustible bio-oil. The remaining gas can fuel a variety of power systems including reciprocating engines, gas turbines, and fuel cells.


It is possible to produce specialty value-added products from livestock manure for marketing to consumers based on the fiber content of the manure. For the most part, the examples given below are either experimental or done on a boutique scale. Most involve extracting and using the solid fiber from manure.

  • Peat moss substitute. Fiber recovered from anaerobic digestion of dairy manure is useful as a plant growth medium. Plant growth trials have shown that, when properly processed, the fiber performs like peat moss for growing container plants.Uses of solid fiber from manure
  • Novelty Fiber products. Farmers and other innovators are finding creative ways to make value-added products from fiber recovered from manure.
    • Nursery pots, manure-fiber based seed starter pots, made with biodegradable composted cow manure.
    • Sculptures made with composted manure and marketed as fertilizing garden art.
    • Paper made from processed manure from a variety of animals, including elephants and cows. The dried manure is rinsed in water, leaving the undigested fiber, which is boiled and mixed with other natural fibers to manufacture a variety of paper products.
  • Building materials. Recovered manure fiber has been included in fiberboard for building construction.

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EPA Memorandum of Understanding with The Water Research Foundation Advancing Nutrient Management Efforts

EPA signed a Memorandum of Understanding (MOU) with The Water Research Foundation (WRF) to accelerate progress on reducing excess nutrients in the nation’s waterways.

The MOU builds on successes achieved through the Nutrient Recycling Challenge, a competition launched by EPA with WRF and others to develop affordable technologies to recycle nutrients from livestock manure. Through the new MOU, EPA and WRF will collaborate with the agricultural community to build capacity and awareness of programs and tools that support watershed and market-based approaches to nutrient management. To accomplish these goals, the MOU aims to:

  • Facilitate greater collaborations between the regulated water community, technology developers and providers, and agricultural producers;
  • Match innovative manure and nutrient management technologies with on-farm testing sites, funders for technology demonstrations, and third-party evaluators;
  • Enable producer-to-producer information exchange regarding technology performance; and
  • Develop and disseminate information on specific topic areas related to manure management and resource recovery and reuse.

View MOU between EPA and WRF.

View EPA News Release.

Learn more about what EPA is doing to address excess nutrients at EPA's Nutrient Policy and Data website.

Learn more about WRF.

Nutrient Recycling Challenge""

EPA has partnered with pork and dairy producers, the U.S. Department of Agriculture (USDA), and environmental and scientific experts to launch the Nutrient Recycling Challenge—a competition to develop affordable technologies that recycle nutrients from livestock manure. Every year, livestock producers manage over one billion tons of manure, which contains valuable nutrients—nitrogen and phosphorus—that plants need to grow. Challenge entrants will develop technologies that extract nutrients from manure to generate products with environmental and economic benefits that farmers can use or sell.

The competition has four phases in which innovators can turn their concepts into designs, and eventually, into working technologies to be piloted on livestock farms. In Phase I, which ended January 15, 2016, EPA received 75 concept papers from around the world, and selected 34 submissions to continue on to Phase II of the challenge. EPA awarded a total of $30,000 in cash prizes to the top ten submissions (four "Winners" and six "Honorable Mentions"). 

Phase II

Phase II of the Nutrient Recycling Challenge is a non-competitive incubation program to support innovators as they develop Technology Designs based on their submitted concepts. Phase II began in October 2016 and is only open to the 34 teams selected in Phase I. EPA and its partners are supporting challenge participants with informational webinars and workshops, opportunities to learn about livestock operations, mentorship, and feedback that can maximize their ability to develop designs for effective and affordable technologies.

Innovators will complete their designs by March 2017 in preparation for Phase III of the challenge, which is expected to be a prize competition for building prototypes based on innovators’ designs. The plan for the fourth and final phase of the challenge is to conduct demonstration pilots of nutrient recovery technologies on real-life farms. 

For more information:

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