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EPA Proposes Revised Clean Water Act Regulations for CAFOs in Response to Waterkeeper Decision

Client Alert | 2 min read | 06.30.06

In today's Federal Register, EPA proposes revised Clean Water Act regulations for CAFOs in response to the 2005 Waterkeeper decision from the Second Circuit that vacated and remanded portions of EPA's 2003 final rule. EPA is proposing to revise the National Pollutant Discharge Elimination System ("NPDES") permitting requirements and the Effluent Limitations Guidelines ("ELGs") for CAFOs. The major aspects of the proposed rule include:

  • In response to the Second Circuit's ruling that EPA cannot require CAFOs to apply for an NPDES permit in the absence of an actual discharge, EPA proposes to require only those CAFOs that "discharge or propose to discharge" to apply for NPDES permit coverage. It is up to individual CAFOs to decide whether or not permit coverage is necessary.
  • EPA proposes to maintain the agricultural stormwater exemption from the 2003 rule, which was upheld by the Second Circuit. EPA rejected the request from citizens' groups to require an NPDES permit for stormwater discharges from land application areas where the CAFO complies with EPA's manure management practices.
  • In response to the Second Circuit's ruling on agency and public review of nutrient management plans ("NMPs"), EPA proposes to require CAFOs seeking NPDES permit coverage to submit their NMPs with the notice of intent for general permit coverage or with the application for an individual permit, and advances several proposals for the agency and public review process. EPA emphasizes that the agency and public review provisions must be structured properly in order to preserve the benefits of a general permitting system.
  • EPA's proposal retains the July 31, 2007 deadline for when permit applications and NMPs will need to be submitted, apparently to emphasize that CAFOs should be developing their NMPs now. The July 2007 deadline may prove controversial, as it may not allow sufficient time for the states to adapt their programs to the revised regulations.

EPA will accept public comments on the proposed rule until August 14, 2006. To see the proposed rule and preamble published today, click here.

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Client Alert | 3 min read | 11.21.25

A Sign of What’s to Come? Court Dismisses FCA Retaliation Complaint Based on Alleged Discriminatory Use of Federal Funding

On November 7, 2025, in Thornton v. National Academy of Sciences, No. 25-cv-2155, 2025 WL 3123732 (D.D.C. Nov. 7, 2025), the District Court for the District of Columbia dismissed a False Claims Act (FCA) retaliation complaint on the basis that the plaintiff’s allegations that he was fired after blowing the whistle on purported illegally discriminatory use of federal funding was not sufficient to support his FCA claim. This case appears to be one of the first filed, and subsequently dismissed, following Deputy Attorney General Todd Blanche’s announcement of the creation of the Civil Rights Fraud Initiative on May 19, 2025, which “strongly encourages” private individuals to file lawsuits under the FCA relating to purportedly discriminatory and illegal use of federal funding for diversity, equity, and inclusion (DEI) initiatives in violation of Executive Order 14173, Ending Illegal Discrimination and Restoring Merit-Based Opportunity (Jan. 21, 2025). In this case, the court dismissed the FCA retaliation claim and rejected the argument that an organization could violate the FCA merely by “engaging in discriminatory conduct while conducting a federally funded study.” The analysis in Thornton could be a sign of how forthcoming arguments of retaliation based on reporting allegedly fraudulent DEI activity will be analyzed in the future....