What Are the Clean Water Act Requirements That Apply to Animal Agriculture?

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A Brief Overview of the Clean Water Act National Pollutant Discharge Elimination System (NPDES) Requirements for Concentrated Animal Feeding Operations

Farms classified as concentrated animal feeding operations (CAFOs) are subject to National Pollutant Discharge Elimination System (NPDES) permitting under the Clean Water Act (CWA) because they are, by definition, “point sources” of pollution. This has been the case since the mid-1970s. Under the CWA, point sources are prohibited from discharging pollutants to the waters of the U.S. except as authorized by an NPDES permit.

To be considered a CAFO, a farm must first meet the definition of an animal feeding operation or AFO. AFOs that meet certain criteria for size and pollution potential are considered to be CAFOs. CAFOs that discharge pollutants into waters of the U.S. must be covered by an NPDES permit. The CAFO regulations are available on the U.S. Environmental Protection Agency (EPA) website in the document “Compiled CAFO Rule“.

The regulations include requirements for CAFO operators to develop a nutrient management plan that includes management measures for both the production area and the land application areas of the operation, as well as record-keeping and reporting requirements.

The video below, produced by the U.S. Poultry & Egg Association summarizes NPDES requirements for CAFOs.

What Is a Point Source and a Non-Point Source of Pollution?

A point source of pollution, as defined in the Clean Water Act is:

Any discernible, confined and discrete conveyance, including but not limited to any pipe, ditch, channel, tunnel, conduit, well, discrete fissure, container, rolling stock, concentrated animal feeding operation, or vessel or other floating craft, from which pollutants are or may be discharged. This term does not include agricultural stormwater discharges and return flows from irrigated agriculture.

The EPA is responsible for administering most elements of the CWA, including the NPDES program. Most states are authorized to issue NPDES permits, including those issued to CAFOs (State NPDES CAFO contacts).

State-specific water quality requirements may also apply to livestock operations. In some cases those measures may be implemented in a “dual purpose” (NPDES + state) permit, or may be implemented solely in state permits. State permits most commonly apply to CAFOs that do not discharge to waters of the U.S. Additional information: The EPA Agriculture Center has compiled information about laws and regulations that apply to animal agriculture and other agricultural activities including cropping, chemical handling, buildings and construction, and fuel as well as requirements for air emissions.

The U.S. Department of Agriculture (USDA) has no regulatory authority for CWA programs but provides technical or financial assistance through the Natural Resources Conservation Service (NRCS) for farms implementing recommended manure management or nutrient planning processes.

In addition to regulations enforced by federal and state agencies, livestock and poultry farms are occasionally subject to rules at the local level such as county zoning. These often address groundwater or wellhead protection as well as odor and nuisance concerns. New farms or those making substantial changes are especially likely to need to check into local zoning requirements before constructing new facilities.

Recommended Resources

EPA Fact Sheets

USDA Natural Resources Conservation Service (NRCS) Agricultural Waste Management Field Handbook Chapter 1: Laws, Regulations, Policy, and Water Quality Criteria

eXension Fact Sheets


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These materials were developed by the Livestock and Poultry Environmental Learning Center (LPELC) with funding from the U.S. Environmental Protection Agency and with input from the Natural Resources Conservation Service, National Cattlemen’s Beef Association, National Milk Producers Federation, National Pork Board, United Egg Producers, and U.S. Poultry and Egg Association.

For questions on these materials, contact Jill Heemstra, jheemstra@unl.edu. All images in this module, unless indicated otherwise, were provided by Jill.

Reviewers: Tetra Tech, Inc.; Paul Goeringer, University of Marlyland; Kent Woodmansey, South Dakota Department of Environment and Natural Resources; Joe Harrison, Washington State University; and Tom Hebert, Bayard Ridge Group