Congress of the United States


Date of this Version



Published by Congressional Research Service, 7-5700,, RL33656


In October 2008, the Environmental Protection Agency (EPA) issued a regulation to revise a 2003 Clean Water Act rule governing waste discharges from large confined animal feeding operations (CAFOs). This action was necessitated by a 2005 federal court decision (Waterkeeper Alliance et al. v. EPA, 399 F.3d 486 (2nd Cir. 2005)), resulting from challenges brought by agriculture industry groups and environmental advocacy groups, that vacated parts of the 2003 rule and remanded other parts to EPA for clarification.

The Clean Water Act prohibits the discharge of pollutants from any “point source” to waters of the United States unless authorized under a permit that is issued by EPA or a qualified state, and the act expressly defines CAFOs as point sources. Permits limiting the type and quantity of pollutants that can be discharged are derived from effluent limitation guidelines promulgated by EPA. The 2003 rule, updating rules that had been in place since the 1970s, revised the way in which discharges of manure, wastewater, and other process wastes from CAFOs are regulated, and it modified both the permitting requirements and applicable effluent limitation guidelines. It contained important first-time requirements: all CAFOs must apply for a discharge permit, and all CAFOs that apply such waste on land must develop and implement a nutrient management plan.

EPA’s 2008 revised regulation addressed those parts of the 2003 rule that were affected by the federal court’s ruling: (1) it eliminated the “duty to apply” requirement that all CAFOs must either apply for discharge permits or demonstrate that they have no potential to discharge, which was challenged by industry plaintiffs; (2) it added procedures regarding review of and public access to nutrient management plans, challenged by environmental groups; and (3) it modified aspects of the effluent limitation guidelines, also challenged by environmental groups. The final rule also modified a provision of the 2003 rule that the court upheld, clarifying the treatment of a regulatory exemption for agricultural stormwater discharges.

EPA’s efforts to revise the 2003 rule were controversial, with particular focus on the “duty to apply” for a permit and agricultural stormwater exemption provisions. Environmental groups strongly criticized EPA’s actions, arguing that the Waterkeeper Alliance court had left in place several means for the agency to accomplish much of its original permitting approach, but instead EPA chose not to do so. Industry groups were generally supportive, approving deletion of the previous “duty to apply” provision and also of efforts to provide flexibility regarding nutrient management plan modifications. Nevertheless, legal challenges to the 2008 revised rule were brought by both industry and environmental groups. State permitting authorities also had a number of criticisms, focusing on key parts that they argued would greatly increase the administrative and resource burden on states. CAFOs were to comply with the revised rule by February 27, 2009. Congress has shown some interest in CAFO issues in the past, primarily through oversight hearings in 1999 and 2001.