Jump to Navigation

EPA Issues Guidance for CAFOs on Scope of Clean Water Act Permitting, Plans Further Rulemaking

July 1, 2010

The Environmental Protection Agency (EPA) recently issued guidance to clarify the permitting obligations of concentrated animal feeding operations (CAFOs) under the Clean Water Act (CWA). The guidance stems from a settlement agreement with environmental groups relating to EPA’s 2008 rule,[1] which requires CAFOs that “discharge” or “propose to discharge” to obtain National Pollutant Discharge Elimination System (NPDES) permits. The rule also allows a CAFO to self-certify that it does not need an NPDES permit, based upon an objective set of criteria. Environmental groups objected to the self-certification option, claiming that it cedes enforcement authority to the regulated community, and that the rule does not do enough to ensure that CAFOs will be covered by NPDES permits. EPA’s guidance elaborates on the circumstances when a CAFO will be deemed to “discharge” or “propose to discharge” to waters within CWA jurisdiction, and so require an NPDES permit. The guidance is only the first step EPA must take to comply with the settlement agreement. EPA also agreed to propose a rule by May 2011 that will require all CAFOs, regardless of whether they require an NPDES permit, to submit detailed information to EPA regarding their operations.


The CWA prohibits the discharge of pollutants from a point source into waters of the United States without a valid permit, such as an NPDES permit.[2] The CWA expressly includes CAFOs in the definition of a “point source,”[3] and EPA has issued detailed rules that define when a facility qualifies as a CAFO.[4] Unlike the typical CWA “point source,” which is a “discrete conveyance,” CAFOs are deemed point sources due to characteristics of the facility as a whole. EPA authorizes nearly all states to implement the NPDES program for CAFOs, but those states must impose requirements that are no less stringent than EPA’s regulations.

EPA has gone through several rounds of rulemaking proceedings focused on when a CAFO has an obligation to obtain an NPDES permit. In 2003, EPA promulgated a rule that required all owners or operators of CAFOs to apply for NPDES permits, unless they could demonstrate that there was no potential to discharge.[5] In response to a lawsuit brought by members of the regulated community challenging this “duty to apply” portion of the rule, the Second Circuit held in 2005, in Waterkeeper Alliance v. EPA,[6] that the CWA does not authorize EPA to require CAFOs to obtain NPDES permits unless there is an actual, rather than a potential discharge.

EPA responded to the Waterkeeper decision with a 2006 proposed regulation that amended the “duty to apply” rule by requiring only CAFOs that “discharge or propose to discharge” to apply for NPDES permits.[7] In 2008, EPA supplemented and finalized that rule[8] to clarify the circumstances when an NPDES permit is necessary. The final rule included a requirement that CAFOs apply for NPDES permits if they discharge or “propose to discharge,” where a CAFO proposes to discharge “if it is designed, constructed, operated, or maintained such that a discharge will occur, not simply such that it might occur.”[9] CAFO owners or operators that elect not to seek an NPDES permit need not confirm with EPA that the facility does not, in fact, discharge or propose to discharge. However, unpermitted discharges would still face potential enforcement under CWA § 301, and liability under a CWA citizen suit, in addition to liability for failing to obtain a permit.

The rule also included a voluntary certification procedure that attempted to provide a structured, objective set of criteria for owners and operators of CAFOs to follow in determining whether they need to apply for a permit. The rule included eligibility criteria that a CAFO must meet to become zero-discharge certified, such as (1) addressing existing physical and operational conditions to ensure that there will not be a waste discharge, and making accommodations to address changes at the facility; (2) developing, implementing, maintaining, and revising, as necessary, a nutrient management plan (NMP) that ensures that no discharges will occur from the facility; and (3) maintaining documentation underlying the certification. The submission of this information automatically certifies the facility – EPA need neither review nor approve the certification or the NMP.[10] Obtaining certification does not protect a CAFO from liability under the CWA if a discharge in fact occurs. However, it creates a rebuttable presumption that the CAFO does not propose to discharge, and is therefore not liable for the separate violation of having failed to obtain a permit.

Settlement Agreement With Environmental Groups

Immediately after EPA issued the final rule, environmental groups petitioned the Ninth Circuit for review of the rule, alleging that the rule allows thousands of CAFOs to avoid obtaining NPDES permits. The lawsuit was consolidated in the Fifth Circuit with seven other petitions challenging the rule. The environmental groups alleged, among other things, that the rule impermissibly allows CAFOs to determine whether they discharge or propose to discharge, and fails to provide adequate regulatory oversight of the veracity of those assertions. EPA resolved these claims in a May 25, 2010 settlement agreement that, in part, required EPA to immediately publish guidance “designed to assist permitting authorities in implementing the [CAFO regulations] by specifying the kinds of operations and factual circumstances that EPA anticipates may trigger the duty to apply for permits as discharging or proposing to discharge.”[11]

EPA’s “Objective Assessment” Guidance

EPA issued its May 28, 2010 guidance, titled “Implementation Guidance on CAFO Regulations – CAFOs That Discharge or Are Proposing to Discharge,” to meet part of its obligations under the settlement agreement. The guidance focuses on the contours of a CAFO’s “objective assessment” of whether it discharges or proposes to discharge, under current regulations, and provides sector-specific guidelines to follow in undertaking this assessment.

The guidance explains that an objective assessment should consider “possible sources of pollutants at the CAFO, such as animal confinement areas; feed storage areas; manure, litter, and process wastewater storage areas; confinement house ventilation fan exhaust; land-applied manure, litter, or process wastewater; and other site specific sources of pollutants, as well as pathways for pollutants from the CAFO to reach waters of the U.S.”[12] Additionally, the guidance clarifies that an objective assessment not only includes “manmade aspects of the CAFO itself,” but should also address climate, hydrology, topography, and other characteristics that are beyond the CAFO operator’s control.[13] Relevant to the consideration are factors such as: proximity to jurisdictional waters; climatic conditions; history of discharges; type and quality of the waste storage system; mortality management; maintenance protocols; drainage of production area; exposure of animal waste and feed to water; and nutrient management planning for land-applications. The guidance provides additional detail regarding four areas of consideration across all animal sectors (animal confinement area; waste storage and handling; mortality management; and land application practices), and addresses design, construction, operation, and maintenance factors that are specific to the dairy, beef, swine, and poultry sectors.

The guidance clarifies that a CAFO that has never previously discharged could still be deemed “proposing” to discharge “due to design and construction of the facility, management practices, or other site-specific characteristics, whether within the CAFO owner/operator’s control or not.”[14] To account for this possibility, the guidance encourages all CAFOs that are deciding whether to seek permit coverage to consider the criteria for the “self-certification” option provided in the 2008 rule, “including a rigorous evaluation of the production area and implementation of a nutrient management plan.…”[15] Even if the CAFO does not pursue the self-certification option, or does not have that option under applicable state regulations, the guidance identifies the certification eligibility criteria as “one basis for making an objective assessment of whether a CAFO discharges or proposes to discharge.”[16] Additionally, the guidance reiterates that the objective assessment process is fluid, and that NPDES permit coverage is required when the CAFO “proposes to discharge.” As a result, EPA recommends that unpermitted CAFOs retain records of operations and maintenance, including drainage maps, operations procedures, inspection records, and records of nutrient management planning and land application protocols, and continually assess whether current circumstances warrant NPDES permit coverage.[17]

Next Steps – Additional Regulations

The guidance is only the first step that EPA will take in complying with the May 2010 settlement agreement. By May 2011, EPA will issue a proposed rule to require all CAFOs, regardless of whether they discharge or propose to discharge, to submit information to EPA that will assist the agency in determining whether an NPDES permit is required. The proposed rule may require CAFOs to submit information regarding the animals housed at the facility, the generation and management of manure, litter, and wastewater, implementation of NMPs, record-keeping, and history of applying for and/or complying with NPDES permits. EPA intends to finalize the proposed rule by May 2012, and will provide the information received for public review. Based on the information received, the environmental groups may petition EPA to promulgate additional rules that would require distinct categories of operations that “presumptively discharge” to seek NPDES permits.

For more information regarding this decision, please contact Meline MacCurdy or any member of Marten Law’s Water Quality practice group.

[1] 73 Fed. Reg. 70418 (Nov. 20, 2008). For a description of the final rule, see M. MacCurdy, EPA Finalizes Long-Awaited CAFO Clean Water Act Rule, Marten Law Environmental News (Dec. 18, 2008).

[2] 33 U.S.C. §§ 1311(a); 1342.

[3] Id. § 1362(14).

[4] Before a facility can be defined as a CAFO it must meet the definition of an “AFO.” 40 C.F.R. § 122.23. An AFO is a “lot or facility” where 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 lots or facility. Id. § 122.23(b). For an AFO to be a CAFO, it must confine more than a threshold number of particular types of animals. Id. Designation as a “Large CAFO” depends exclusively on the number of animals. Id. § 122.23(b)(4). “Medium CAFOs” confine fewer animals than Large CAFOs and either 1) Discharge pollutants into waters of the United States through a man-made ditch, flushing system, or other similar man-made device; or 2) discharge pollutants directly into waters of the United States which originate outside of and pass over, across, or through the facility or otherwise come into direct contact with the confined animals. Id. § 122.23(b)(6). In certain circumstances, any AFO may also qualify as a CAFO if an authorized entity determines that a facility “is a significant contributor of pollutants to waters of the United States.” Id. § 122.23(c).

[5] 68 Fed. Reg. 7176 (Feb. 12, 2003).

[6] 399 F.3d 486 (2d Cir. 2005).

[7] 71 Fed. Reg. 37744 (June 30, 2006).

[8] 73 Fed. Reg. 12321, 12324 (Mar. 7, 2008); 73 Fed. Reg. 70418 (Nov. 20, 2008). For a description of the supplemental proposed rule, see M. MacCurdy, EPA Taking Comments on Proposed CAFO Wastewater Discharge Rule, Marten Law Environmental News (Mar. 26, 2008).

[9] 73 Fed. Reg. 70423 (codified at 40 C.F.R. § 122.23(d)).

[10] Id. at 70426-27 (codified at 40 C.F.R. § 122.23(j)).

[11] Settlement Agreement at 2.

[12] EPA, Implementation Guidance on CAFO Regulations – CAFOs That Discharge or Are Proposing to Discharge (May 28, 2010).

[13] Id. at 2.

[14] Id. at 3.

[15] Id.

[16] Id.

[17] Id. at 4.

This article is not a substitute for legal advice. Please consult with your legal counsel for specific advice and/or information. Read our complete legal disclaimer.