National Pork Producers Council v. United States Environmental Protection Agency, 635 F.3d 738

EPA revised CAFO regulations in 2003 and 2008 under the Clean Water Act (CWA); Waterkeeper challenged the 2003 Rule, prompting appellate review in Waterkeeper Alliance, Inc. v. EPA, 399 F.3d 486 (2d Cir. 2005).
In 2008, EPA issued a Rule and three guidance letters addressing CAFO permit requirements, including liability for failing to apply and land-application NPDS permit terms; petitions for review followed in multiple circuits and were consolidated here.
CAFOs are facilities with animals confined for 45 days in a 12-month period and may discharge pollutants; NPDES permits govern discharges to navigable waters, with agricultural stormwater discharges generally exempt.
The 2003 Rule required CAFOs to apply for an NPDES permit based on a “potential to discharge,” and mandated site-specific Nutrient Management Plans (NMPs) not reviewable or incorporated into permits.
Waterkeeper held that the EPA cannot require CAFOs to apply based on potential discharges, and that NMP terms must be included in permits; the 2008 Rule sought to respond, including liability for failing to apply and land-application provisions.
The Fifth Circuit ultimately vacated the portions of the 2008 Rule imposing a duty to apply on non-discharging CAFOs and the failure-to-apply liability, while upholding certain land-application NMP requirements and permitting authority over land-application terms.

Issue	Plaintiff's Argument	Defendant's Argument	Held
Whether the EPA may impose a duty to apply for a permit on CAFOs that do not discharge	Waterkeeper prevents any duty to apply for non-discharging CAFOs.	EPA may require CAFOs that discharge or propose to discharge to apply.	Duty to apply for non-discharging CAFOs is ultra vires.
Whether imposing liability for failing to apply for a permit lies within the CWA	CWA lacks authority to penalize failing to apply for coverage.	EPA can impose penalties for noncompliance under §1319.	Liability for failing to apply is outside the statute.
Whether land-application requirements must be incorporated as enforceable effluent limitations in NPDES permits	NMP terms are statutory effluent limitations and must be included.	NMP terms were not required to be permit terms.	NMP terms must be incorporated into permits; land-application regulation remains permissible.
Whether the EPA Letters addressing enforcement were final agency actions subject to review	EPA Letters constitute final rules affecting rights and require notice and comment.	Letters merely reiterate existing law and are not final agency actions.	Letters are not reviewable final actions; jurisdiction to review is lacking.

Waterkeeper Alliance, Inc. v. Environmental Protection Agency, 399 F.3d 486 (2d Cir. 2005) (held EPA cannot require CAFOs to apply based on potential to discharge and that NMP terms must be included in permits)
S.D. Warren Co. v. Maine Bd. of Envtl. Protection, 547 U.S. 370 (2006) (discharge triggering permit responsibility requires actual addition of a pollutant)
Natural Resources Defense Council, Inc. v. Environmental Protection Agency, 859 F.2d 156 (D.C. Cir. 1988) (agency authority limited to regulating discharge, not CAFOs themselves)
Service Oil, Inc. v. Environmental Protection Agency, 590 F.3d 545 (8th Cir. 2009) (penalties limited to unlawful discharges; cannot penalize failure to apply)
Bennett v. Spear, 520 U.S. 154 (1997) (two-part final-action test for agency action)
Chevron U.S.A., Inc. v. Natural Resources Defense Council, Inc., 467 U.S. 837 (1984) (cedes deference to agency interpretations when statute is ambiguous)
Waterkeeper Alliance, Inc. v. Environmental Protection Agency, IS NOT TO BE REPEATED (2005) (not to be repeated)