Updated 12/11/09

Compliance and Enforcement National Priority:

Concentrated Animal Feeding Operations (CAFOs)

The United States Environmental Protection Agency’s (EPA) Office of Enforcement and 

Compliance Assurance (OECA) established several national priorities for federal fiscal years 

(FY) 2008 through 2010. Among these priorities, OECA and the ten EPA Regions continue to

make concentrated animal feeding operations (CAFOs) a Clean Water Act (CWA) priority for 

compliance monitoring, compliance assistance, and enforcement through at least FY 2010.

CAFOs have been regulated under the National Pollutant Discharge Elimination System 

(NPDES) program since the mid-1970s. In February 2003, EPA promulgated new CAFO 

regulations to update the NPDES program and prevent environmental harm from these 

operations through better animal waste management. The 2003 regulations required all CAFOs 

to seek NPDES permit coverage. Because of the 2005 decision by the U.S. Court of Appeals for 

the Second Circuit in Waterkeeper v. EPA (399 F.3d 486), EPA can only require CAFOs which 

discharge or propose to discharge to apply for a NPDES permit. In November, 2008, EPA 

revised its CAFO regulations regarding the submission of permit applications and the

development of nutrient management plans to address the Waterkeeper decision mandates. 

Environmental Problem

An ongoing trend toward fewer but larger farm operations, more intensive animal production 

methods, and larger volumes of waste within small geographic areas have heightened CAFOs’ 

environmental and public health impacts. Additionally, many large operations do not have 

sufficient cropland necessary to properly apply all of the manure as fertilizer. The U.S. 

Department of Agriculture estimates that operations which confine livestock and poultry animals 

generate about 500 million tons of manure annually – three times EPA’s estimate of 150 million 

tons of human sanitary waste produced annually in the U.S. Under Section 305(b) of the CWA, 

states have consistently identified agricultural sources - including CAFOs - as a leading 

contributor of water quality impairment in state assessed surface waters. 

Pollutants associated with animal waste primarily include nutrients - mainly nitrogen and 

phosphorus. However, animal waste may also include organic matter, solids, pathogens, 

pesticides, antibiotics, hormones, salts and various trace elements (including metals). 

Improperly managed manure and wastewater can release pollutants into the environment through 

several pathways, such as through runoff from animal confinement areas, manure storage areas, 

and/or from cropland where manure is applied as fertilizer. 
Why OECA is Addressing the Problem 

OECA continues to focus on CAFOs as a CWA national enforcement priority due in part to 

potential risks from CAFOs’ inadequate manure management, a pattern of CWA noncompliance 

in the industry, and the need for EPA leadership in implementing the federal CAFO regulations. 

The 2005 Waterkeeper decision narrowed the universe of CAFOs required to obtain permits to 

those facilities that discharge, or propose to discharge. In addition to narrowing the scope of 

who is required to seek permits, EPA’s revised 2008 CAFO regulations and strategy clarify that 

the CWA and the federal regulations prohibit discharges from a CAFO, even one that is 

unplanned or accidental, unless it is authorized by the terms of a permit. Any facility that meets 

the regulatory definition of a “CAFO” as it was defined in the 1976 rule and discharges, needs a 

NPDES permit now. 

How the Problem will be Addressed

Because it is impossible for EPA to identify and address all CAFOs that have unauthorized 

discharges, the Agency, along with its state partners, will engage in strategically targeted 

inspections and enforcement actions. The Agency’s strategy is to have EPA Regions work 

closely with state partners to identify specific geographic areas where CAFOs are having, or may 

have, a serious environmental or human health impact. EPA expects that the targeted CAFO 

universe will generally consist of large and medium CAFOs that are discharging, or are 

designed, operated, or maintained such that a discharge to a water of the United States is likely to 

occur. 

EPA will continue to refine its understanding of the CAFO universe, improve targeting of 

compliance and enforcement activities to increase CAFO NPDES permit coverage and 

compliance, and assess and communicate the effectiveness of its actions. EPA believes ensuring 

CAFOs that need permits obtain them is critical to improving manure management and 

addressing the environmental problems associated with this industry.

EPA considers individual state commitments to CAFO permitting a critical component to 

achieving a level playing field. EPA will seek to ensure that state NPDES programs are 

comparable to federal standards, CAFO permits are being issued, and CWA non-compliance 

issues are being identified and remedied.

Federal efforts will also address CAFOs that have NPDES permits and are in violation of their 

permit requirements. EPA’s strategy seeks to ensure that CAFO permit coverage results in 

proper manure management.
Highlights from the Previous Cycle

EPA has established an internal national CAFO work group to provide a forum for discussing 

CAFO compliance and enforcement issues and identifying training needs. OECA has provided 

and continues to develop additional technical training to support EPA Regions in the 

development of CAFO CWA cases.

Through FY 2008, EPA has conducted over 1,100 inspections (EPA-only inspections and 

EPA/state joint inspections) and completed 244 federal enforcement actions against CAFOs for 

CWA violations. Federal enforcement actions have resulted in CAFOs spending more than 53 

million dollars on corrective measures and a reduction of over 64 million pounds of pollutants 

that would have otherwise been discharged.

A number of EPA Regions are using a variety of sampling and modeling tools to develop cases 

against existing CAFOs with unauthorized discharges. Recent EPA enforcement actions reflect 

the high level of sophistication with which some Regions are conducting CAFO compliance 

investigations.