The 2003 rule was challenged by multiple parties—environmental groups and agriculture industry groups—and in February 2005, a federal court issued a ruling that upheld major parts of the rule, vacated other parts, and remanded still other parts to EPA for clarification, leaving all parties unsatisfied to at least some extent. Industry groups challenged the 2008 revised rule, and in March 2011, a federal court vacated a portion of that regulation. The 2003 Rule

The CWA prohibits the discharge of pollutants from any "point source" to waters of the United States unless authorized under a national pollutant discharge elimination system (NPDES) permit that is issued by EPA or a qualified state. NPDES permits limit the type and quantity of pollutants that can be discharged from a facility and specify other requirements, such as monitoring and reporting. The specific discharge limitations in the permit are derived from effluent limitation guidelines and standards (ELGs) that are separately promulgated by EPA for specific categories of industrial sources. The act expressly defines CAFOs as point sources. The 2003 rule did not redefine what a CAFO is, but it revised the way in which discharges of manure, wastewater, and other process wastes from CAFOs are regulated, and it modified both the NPDES permitting requirements and applicable ELGs. The Waterkeeper Alliance Decision and EPA's 2008 Revised Rule

The 2003 rule was challenged in court by a number of groups. Environmental groups, on the other hand, strongly criticized the proposal, arguing that the Waterkeeper Alliance court left in place several means for the agency to accomplish much of its original permitting approach, but instead EPA chose not to do so. They focused on key parts that they argued would greatly increase the administrative and resource burden on states. The issues are (1) the "duty to apply" requirement, which was challenged by industry plaintiffs; (2) procedures regarding review of and public access to nutrient management plans, challenged by environmental groups; and (3) aspects of the effluent limitation guidelines, also challenged by environmental groups. Duty to Apply for a Permit

The "duty to apply" provisions of the 2003 rule were among the most controversial, and they remained so, even as revised in 2008—farm industry groups' challenge to the 2003 rule focused on this requirement and, as discussed below, so did these groups' subsequent challenge to the 2008 revised rule. The environmental plaintiffs argued to the federal court that the NMP part of the 2003 rule was unlawful under the Clean Water Act and the Administrative Procedure Act because it failed to require that the terms of the NMP must be reviewed and be included in the NPDES permit (inclusion in the permit would make the NMP enforceable by the government and private citizens) and because it allowed permitting authorities to issue permits in the absence of any meaningful government or public review of this aspect of the permit. Agricultural Stormwater Discharges

One issue that the federal court upheld in 2005 concerns the rule's treatment of a regulatory exemption for agricultural stormwater discharges. In the earlier litigation on the 2003 rule, agriculture industry groups had challenged a provision of that rule that explicitly required all CAFOs to apply for an NPDES permit, or to demonstrate that they have no potential to discharge. In July 2012, EPA modified the 2008 CAFO regulations to conform to the court's 2011 ruling. Both agriculture groups and environmental groups criticized EPA's proposal. Congressional Interest

Congress has shown some interest in CAFO issues in the past, primarily through oversight hearings in 1999 and 2001, before issuance of the 2003 and 2008 CWA rules.
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). The 2008 action was necessitated by a 2005 federal court decision (Waterkeeper Alliance et al. vs. 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 2008 rule also modified a provision of the 2003 rule that the court upheld, clarifying the treatment of a regulatory exemption for agricultural stormwater discharges. CAFOs were to apply for permits and develop nutrient management plans by February 2009. After that date, sources had three years to actually get permit coverage.
EPA's efforts to revise the 2003 rule were controversial, particularly regarding 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. 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 state regulators. Farm industry groups were generally supportive of the 2008 rule. Nevertheless, some of them brought a legal challenge. In 2011, a federal court agreed with the industry petitioners and vacated a portion of the 2008 rule concerning the "duty to apply" requirement. EPA revised the rule in 2012 in response to this ruling. Environmental groups have initiated several legal actions as they continue to criticize most of EPA's efforts to reduce pollution from CAFOs. Congress has shown some interest in CAFO issues in the past, primarily through oversight hearings before issuance of the 2003 and 2008 rules.