Agriculture and the Ripple Effects of City & County of San Francisco v. EPA

In March, the U.S. Supreme Court added a new twist to the Clean Water Act (CWA) with its decision in City and County of San Francisco, California v. EPA, 145 S. Ct. 704 (2025). Though the case may seem urban, the Court’s decision could have ripple effects across rural America—especially the agricultural sector.

Background

The City of San Francisco operates a combined treatment facility, which treats wastewater from 250,000 residents before discharging it into the Pacific Ocean. This can be problematic during heavy rains, where stormwater exceeds the facility’s capacity, leading to untreated public wastewater and stormwater escaping into the ocean. As a pollutant discharging facility, Oceanside had received and renewed its NPDES permit for years. However, in its 2019 permit, the Environmental Protection Agency (EPA) added two limitations that focus on the receiving water quality rather than the discharged water quality. This meant San Francisco could follow all the requirements of their permit but still violate the permit if the receiving body of water (the ocean) fell below acceptable limits.

San Francisco challenged these provisions of their NPDES permit, alleging the end-result limitations exceed the EPA’s authority. The Supreme Court eventually held that the Clean Water Act (CWA) does not authorize the EPA to penalize permittees based on the water quality of receiving waters through such end-result provisions. In the Court’s view, the receiving waters should not be impaired if the EPA sets specific enough requirements for NPDES permittees to follow.

Regulatory History

The CWA prohibits “the discharge of any pollutant” into Waters of the United States (WOTUS) without a permit. The National Pollutant Discharge Elimination System (NPDES) provides a variety of permits which allow such discharges. With an NPDES permit, entities can discharge certain pollutants in specific amounts into WOTUS.

Relevant here, the Court describes three different types of CWA provisions addressing effluent limitations. First, NPDES permits impose technology-based effluent limitations (TBELs), which require a minimum level of treatment of a pollutant before the pollutant can enter a body of water. Second, when TBELs are insufficient to protect water quality, an NPDES permit can also include water quality-based effluent limitations (WQBELs), which prohibit any pollutant discharges that would unduly impair water quality. Third, permits often include non-numerical limitations on pollution, such as requiring the permittee to follow “best practices.”

Failure to comply with NPDES permit requirements can result in civil penalties or even criminal prosecution. The “permit shield” doctrine protects permittees: if they comply with their permit, they are deemed in compliance with the CWA, even if water quality standards are not fully met.

The Court upheld all three of these mechanisms, including non-numerical limitations. However, it held that the EPA exceeded its authority by imposing "end-result" requirements in NPDES permits. The Court explained that these requirements made permittees responsible for ensuring that receiving water bodies met applicable water quality standards without specifying concrete actions or pollutant limits. The Court determined that such provisions are too speculative and that EPA must provide specific guidelines on what permit holders can and cannot do. In San Francisco’s case, the EPA’s requirements—not to “contribute to a violation of any applicable water quality standard for receiving waters” or to perform any treatment or discharge that creates pollution, contamination or nuisance under state law—were too vague and backward looking. Simply put, the EPA cannot regulate the “end” result without specifying the “means.”

What does this decision mean for agriculture?

CWA and NPDES permits are not only for California water treatment plants. The CWA regulates agriculture in multiple ways. The CWA includes “agricultural waste” in its definition of a pollutant, and “concentrated animal feeding operations” may be considered a point source under 33 U.S.C. § 1262 if they discharge. The Fifth Circuit held in National Pork Producers Council v. EPA, 635 F.3d 738 (5th Cir. 2011) that the EPA can only require a CAFO to obtain an NPDES permit if it actually discharges. In NPPC v. EPA, the Court specified that the EPA cannot require a CAFO to obtain an NPDES permit for only proposed or speculative discharges. For example, CAFO-sized CFOs in Indiana do not require NPDES permits because Indiana prohibits livestock farms from discharging any manure.

Ag operations may also fall into the agricultural stormwater exemption as “non-point source” runoff, where pollutants only reach a body of water because of precipitation. The CWA also influences how the EPA issues pesticide applicator permits and construction permits in wetland areas.

The San Francisco decision limits the EPA's ability to hold agricultural NPDES permit holders accountable for the overall quality of downstream waters, focusing instead on specific discharge limitations of the permittee. Permits now should include precise effluent limitations rather than vague non-numerical quality standards for receiving waters. In theory, this should make compliance more straightforward for ag operators. In some states, this could also cause state regulators to increase regulatory oversight to fill the supposed gap left by the San Francisco decision or decrease regulation to match federal standards.

Operations outside the realm of NPDES permits are not entirely off the hook because there is another CWA challenge to keep on the radar. The Lucas County Commissioners in Toledo, Ohio initiated a suit against the EPA last May for the agency’s failure to address algal blooms in Lake Erie. The County alleges that the agricultural stormwater exemption is to blame. We will keep an eye as this case moves forward. With the Court removing end-result provisions from the EPA’s regulatory toolkit, the agency may pivot toward imposing new permitting requirements on previously exempt farming operations—especially if the agricultural stormwater exemption challenge is successful.

Thank you to our summer law clerk, Kaleigh Shaw, for her work on this article.