The NPDES is a program enacted by the EPA pursuant to the Clean Water Act to regulate pollutants discharged from “point sources” into waters of the United States.[1]
An NPDES permit is a license for a facility to discharge a specified amount of a pollutant into waterways under certain conditions. The permit contains limits on what can be discharged, requirements for monitoring and reporting, and other provisions intended to ensure that the discharge does not harm water quality.[2] Effluent (liquid waste or sewage) limitations serve as the primary mechanism in NPDES permits and these are based on guidelines established by the EPA.[3]
A permit can be issued by the EPA or by state, tribal, and territorial governments that are authorized to implement their own NPDES programs which can be more, but not less, stringent than EPA guidelines.
Currently 47 states and one territory are authorized to implement the NPDES program.[4]
40 CFR Subpart A – Definitions and General Program Requirements §§ 122.1 – 122.7
[“Point source means 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, landfill leachate collection system, vessel or other floating craft from which pollutants are or may be discharged. This term does not include return flows from irrigated agriculture or agricultural storm water runoff.” § 122.3]U.S. EPA (2024) National Pollutant Discharge Elimination System (NPDES), About NPDES, https://www.epa.gov/npdes/about-npdes
U.S EPA (2024) National Pollutant Discharge Elimination System (NPDES), NPDES Permit Limits. https://www.epa.gov/npdes/npdes-permit-limits
U.S. EPA (2024) National Pollutant Discharge Elimination System (NPDES), NPDES State Program Authority. https://www.epa.gov/npdes/npdes-state-program-authority
No. Only animal feeding operations (AFOs) that meet the EPA’s definition of a concentrated animal feeding operation (CAFO) can potentially be regulated under the NPDES program. An AFO is designated by the EPA as a CAFO either because it exceeds certain animal number thresholds, or because, regardless of size, it is determined to be a significant contributor of pollutants to waters of the U.S.[1]
However, there is no general duty by a CAFO to apply for a permit. And even the EPA acknowledges that many CAFOs “continue to discharge without NPDES permits because successive court decisions have severely limited EPA’s ability to require CAFOs to obtain an NPDES permit. While many waters are affected by pollutants from CAFOs, many CAFOs often claim that they do not discharge, and EPA and state permitting agencies lack the resources to regularly inspect these facilities to assess these claims, particularly since discharges often only occur during certain weather conditions. In addition, the regulations contain definitions, thresholds and limitations that make it difficult to compel permit coverage, limit the discharge of pollutants under certain circumstances, and enforce requirements even when discharges have been established.”[2]
Moreover, an unpermitted CAFO can self-certify that it does not discharge, and this certification is not reviewable by the federal or state permitting authority.[3]
40 CFR § 122.23(c) EPA Administered Permit Programs: The National Pollutant Discharge Elimination System, Concentrated animal feeding operations.
U.S. EPA (May 2022) EPA Legal Tools to Advance Environmental Justice, EPA Publication No. 360R22001, p. 75.
U.S. EPA (2008) Regulation and Effluent Limitations Guidelines for CAFOs in Response to the Waterkeeper Decision, 73 Fed. Reg. 70418, 70426. [“EPA has concluded that providing a voluntary option for unpermitted CAFOs to certify to the Director that the CAFO does not discharge or propose to discharge based on an objective assessment of the CAFO’s design, construction, operation, and maintenance is reasonable and appropriate for CAFOs.”] [“A CAFO’s no discharge certification is not subject to review by the permitting authority in order for it to become effective and the permitting authority is not required to make the certification available to the public for comment because the certification is not a permit application for which review is required under section 402 of the CWA.”]
At the end of 2023, the EPA lists 6,174 CAFOs with NPDES permits. The agency estimates that there are 21,179 EPA-defined CAFOs in the U.S.[1]
There are vast differences in state protocols for implementing NPDES permits. For instance, in Oregon anyone operating an enclosed animal operation regardless of the size of the establishment is required to apply for a permit.[2] In Iowa, where the EPA estimates there are more than 4,000 EPA-defined CAFOs, only 157 have permits. And in Indiana, Idaho, Arkansas, and New York where there are more than 2,100 EPA-defined CAFOs, none have permits.[3,4]
US EPA (May 2024) NPDES CAFO Permitting Status Report: National Summary, End year 2023 https://www.epa.gov/npdes/npdes-cafo-regulations-implementation-status-reports [“Reports include the total number of CAFOs, and the number of CAFOs with NPDES permits for each state.”]
Oregon Dept. of Agriculture, Chapter 603, Confined Animal Feeding Operation Program. https://secure.sos.state.or.us/oard/displayDivisionRules.action?selectedDivision=2751
NPDES CAFO Permitting Status Report, End year 2023
For definition of EPA-defined CAFO see, Defining AFOs & CAFOs
Yes. However, the agency acknowledges that “many CAFOs are not regulated and continue to discharge without NPDES permits because successive court decisions have severely limited EPA’s ability to require CAFOs to obtain an NPDES permit.”[1]
In 2003, recognizing the threats all CAFOs pose to water quality, the EPA enacted a rule that required any CAFO either to apply for an NPDES permit or to demonstrate that it did not have the potential for discharge.[2] This rule was challenged by the meat industry, and in 2005, that part of the rule was vacated by the U.S. Court of Appeals for the Second Circuit (the Waterkeeper decision) on the grounds that the EPA did not have regulatory authority over a CAFO before there is a discharge of pollutants.[3]
In response to the Waterkeeper decision, the EPA removed the “duty to apply” and required only that a CAFO discharging or proposing to discharge pollutants seek an NPDES permit.[4] However, another federal court vacated that portion of the rule that required a CAFO proposing to discharge first obtain a permit.[5] And the EPA revised the regulations again to require a CAFO seek a permit only if there is an actual discharge of pollutants into navigable waters.[6]
U.S. EPA (2022) EPA Legal Tools to Advance Environmental Justice, Pub. No. 360R22001, p. 75.
U.S. EPA (2003) National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitation Guidelines and Standards for Concentrated Animal Feeding Operations (CAFOs), 68 Fed Reg. 7176, 7181.
Waterkeeper Alliance et al. v EPA, 399 F3rd 486, 2nd Cir. (2005).
U.S. EPA (2008) Revised National Pollutant Discharge Elimination System Permit Regulation and Effluent Guidelines for Concentrated Animal Feeding Operations in Response to the Waterkeeper Decision, 73 Fed. Reg. 70418, 70426.
National Pork Producers Council v. EPA, 635 F.3d 738 (2011).
Leah Hurtgen Ziemba (2012) Federal CAFO Regulations Remove “Propose to Discharge” Permitting Requirement, National Law Review. And see, U.S. EPA (2024) Animal Feeding Operations – Regulations, Guidance, and Studies, Regulations 2012, Compiled CAFO Rule (July 30, 2012).
Yes. While acknowledging some of the restrictions placed on the EPA by the courts, a nationwide coalition of citizen and environmental groups filed a petition in 2017 requesting that the EPA revise its still-weak regulations for CAFOs.[1] The petition included a number of requests, including one that the EPA revise its interpretation of the agricultural stormwater exemption to rule that no discharges from CAFOs be exempt as non-point source pollution. Another request included a requirement for water quality monitoring in NPDES permits. The petition also asked for a revision of the category Medium CAFO since operators of AFOs were skirting environmental regulations by maintaining animal numbers just under the Large CAFO threshold size.[2]
When, after five years, the EPA had not responded to the petition, the coalition sued the EPA to force the agency to respond.[3]
Finally, in answer to the lawsuit in 2023, the EPA announced that because it had so little data on the impacts of CAFO’s on “waters of the United States,” it would gather information concerning discharges from CAFO production areas and land application. But cautioning that because of its limited resources, lack of sufficient understanding of technologies and practices that have developed since its earlier rulings, and more pressing priorities, the agency implied that it could take several years before deciding whether to revise CAFO regulations.[4]
Food & Water Watch v. EPA (2017) Petition to Revise the Clean Water Act Regulations for Concentrated Animal Feeding Operations. https://www.foodandwaterwatch.org/wp-content/uploads/2021/06/citizens_cafo_cwa_petition.pdf
(2017) Petition to Revise the Clean Water Act Regulations for Concentrated Animal Feeding Operations. p. 31.
Food & Water Watch (October 11, 2022) After Long Delay, Groups Sue EPA for Response on Factory Farm Water Pollution Rules. [In 2022, another coalition filed a petition requesting the EPA adopt a rebuttable presumption (an assumption that is taken to be true unless someone proves otherwise) that large CAFOs using wet manure management systems do, in fact, discharge pollutants. Petitioners cited to the EPA’s own admission that many CAFOs do discharge and that the current regulations do not allow for effective enforcement. (Earthjustice.org [October 2022] Petition to Adopt a Rebuttable Presumption that Large CAFOs Using Wet Manure Management Systems Actually Discharge Pollutants Under the Clean Water Act, p. 1)] [A federal court later denied a subsequent petition to compel the EPA to respond to the 2017 petition. See, Food & Water Watch, et al. vs. EPA, No. 23-2146 (9th Cir. 2024)]
U.S. EPA (2023) Effluent Guidelines Program Plan 15, EPA-821-R-22-004, p. A-3. [“Completing this study before determining whether to revise the ELG also reflects EPA’s careful evaluation of the Agency resources that would need to be committed to a rulemaking, due to the large number of environmental priorities that EPA has concluded need to be addressed through rulemaking. Typical ELG rulemakings take several years, 3 full-time employees, and a million dollars per year in contractor support.”]
Yes. Citizens and citizen groups may petition the EPA to withdraw a state’s authority to administer the NPDES program. Since September 1989, there have been numerous petitions, none of which have resulted in a program withdrawal.[1] Not all petitions, however, are related to CAFOs.
U.S. EPA (July 30, 2024) NPDES State Program Withdrawal Petitions. https://www.epa.gov/npdes/npdes-state-program-withdrawal-petitions
Written permits address the specific characteristics of a facility, often on a case-by-case basis. At a minimum, NPDES regulations identify monitoring, record-keeping, and reporting requirements that are applicable to a permitted CAFO.[1]
Large permitted CAFOs may have additional requirements, e.g., visual inspections of the production area and soil analysis of land applied manure. They must also keep records of the inspections, estimated amounts of manure and wastewater generated per year, and the off-site transfer of manure.[2]
At present, a CAFO is not required to monitor pollutants in runoff water from land application areas or underground discharges from waste containment structures.[3] However, in 2021, a federal court pointed out that when a permit forbidding underground discharges from production areas (e.g., manure lagoons or pits) and dry weather discharges from land application areas has no coexisting monitoring requirements for the runoff, there is no way to ensure the CAFO is complying with the permit requirements.[4] To date, the EPA has not revised its regulations to address that decision.
40 CFR § 122.41 EPA Administered Permit Programs, The National Pollutant Discharge Eliminations System, Conditions applicable to all permits
U.S. EPA (2012) NPDES Permit Writers’ Manual for Concentrated Animal Feeding Operations, EPA 833-F-12-001, pp. 4-37.
U.S. EPA (2003) National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitation Guidelines and Standards for Concentrated Animal Feeding Operations (CAFOs), 68 Fed Reg. 7176, 7217. [“In this final rule, EPA is continuing to reject imposing surface water monitoring requirements on CAFOs through the effluent guidelines because of concerns regarding the difficulty of designing and implementing through a national rule an effective surface water monitoring program.”]
Food & Water Watch v. EPA, 13 F.4th 896 (9th Circ. 2021) [“The Idaho Permit forbids underground discharges from production areas and dry weather discharges from land application areas. However, the Permit contains no monitoring requirements for either kind of discharge. Because the Permit does not require monitoring that would ensure compliance with its effluent limitations, the EPA’s issuance of the Permit was arbitrary, capricious, and a violation of law.” pp. 26-27]
Enforcement and compliance actions for CAFOs appear to be declining.
In 2018, the EPA terminated its CAFO violation enforcement (“Preventing Animal Waste from Contaminating Surface and Ground Water”) from its enhanced inspection and enforcement program – the National Compliance Initiative (NCI) – and returned it to EPA’s more basic “core” program. The agency explained that court rulings had “narrowed the universe of facilities required to be permitted.”[1]
Data as of 2018 showed that the annual number of inspections at CAFOs had declined from 291 (in 2012) to 109 (in 2018) – a drop of 63%. Similarly, the number of concluded enforcement actions declined within the same time period from 55 to 18 – a drop of 67%.[2] This is hard to understand since prior to 2018, animal waste had been included in the National Compliance Initiatives, where the EPA focuses its resources on the most serious environmental violations.[3]
The EPA currently publishes web data on all its enforcement and compliance actions by type of violation and by facility on its Enforcement and Compliance History Online (ECHO) interactive map.[4]
U.S. EPA (2021) Former National Compliance Initiative: Preventing Animal Waste from Contaminating Surface and Ground Water. https://19january2021snapshot.epa.gov/enforcement/former-national-compliance-initiative-preventing-animal-waste-contaminating-surface-and_.html [Note: This page of EPA’s website is not current and is available as historical material reflecting the EPA website as it existed on January 19, 2021]
U.S. EPA (2021) Former National Compliance Initiative [see, chart at Annual Number of Inspections and Concluded Enforcement Actions at CAFOs]
U.S. EPA (2021) Former National Compliance Initiative: Preventing Animal Waste from Contaminating
Surface and Ground Waste.U.S. EPA Enforcement and Compliance History Online (ECHO) interactive map. Available at https://echo.epa.gov/facilities/facility-search?mediaSelected=all