For a second year in a row, the U.S. Supreme Court has issued rulings that have significantly altered the landscape of environmental law. Most recently, the Supreme Court waded into the waters of the Clean Water Act (“CWA”) with the Court’s 5-4 decision in City and County of San Francisco v. EPA (2025) 145 S.Ct. 704 (“San Francisco v. EPA”). In the March 4, 2025 opinion, the Court found the Environmental Protection Agency (“EPA”) had exceeded its authority under the CWA in its use of “end-result” requirements for National Pollutant Discharge Elimination System (“NPDES”) permittees, which make the permittee responsible for the water quality of the body of water into which the permittee discharges pollutants. In the wake of the ruling, the California State Water Resources Control Board (“State Water Board”) recently issued interim guidance on July 31, 2025, upholding end-result requirements as a valid limitation for Municipal Separate Storm Sewer System (“MS4”) NPDES permits. As a result of the lawsuit and resulting California guidance, it is unclear how the EPA will respond and how other states will manage their MS4 NPDES permits in light of the San Francisco v. EPA ruling.
The CWA creates the comprehensive statutory scheme by which entities are permitted to discharge pollutants into navigable waters. Central to that scheme is the NPDES permit program, through which the EPA and authorized state agencies sets forth effluent limitations and impose monitoring, testing, recordkeeping, and reporting requirements on permittees in order to minimize pollution. The NPDES permit program gives the EPA a broad range of tools to ensure applicable water quality standards under the NPDES permit are met. NPDES permittees that comply with the permit terms are shielded from liability from enforcement by the state enforcement agency, EPA, or citizens under the CWA’s “permit shield” provision.
At issue in San Francisco v. EPA was the EPA’s use of “end-result” provisions in the NPDES permit issued to San Francisco for its two combined stormwater and sewer systems. San Francisco brought this case to challenge the validity of two NPDES Permit prohibitions: (1) a prohibition against contributing to a violation of any applicable receiving water quality standards and (2) a prohibition against any discharge that creates pollution, contamination or nuisance. The first prohibition made any water quality violation in the water receiving the wastewater discharge was considered a violation of the City’s NPDES Permit while the second made any discharge that causes pollution a violation of the City’s NPDES Permit. San Francisco argued these prohibitions created vague and unattainable obligations, as it made the city liable to enforcement by the state enforcement agency, EPA, or citizens for pollutants outside of the city’s control.
The Court agreed with San Francisco, holding that CWA 301(b)(1)(C) did not authorize the EPA to include a NPDES permit term that imposed requirements based on the “end result” – i.e., the quality of the body of water that receives the wastewater. The Court, relying on textual analysis of the CWA as well as its legislative history, concluded that the EPA was authorized only to create limitations that would meet water quality standards, as opposed to open-ended mandates tied to water quality. Because end-result requirements inherently incorporate the water quality standards, the Court found they cannot be a means to implement those same standards. Additionally, the Court determined that this type of requirement was impermissible because it was not possible to determine where the source of the pollution came from. Noting that problems arise when more than one NPDES permittee is authorized to discharge pollutants, such a requirement undermines the CWA’s permit shield provision by making an entity liable for pollution-related harms it had not caused.
The holding of San Francisco v. EPA has had ripple effects at state water agencies, including California. In response, the State Water Board issued interim guidance on July 31, 2025, for Municipal Separate Storm Sewer System (“MS4”) NPDES permits. Despite the holding invalidating the use of end-result limitations, the interim guidance determined such limitations permissible requirements in MS4 permits.
In its reasoning, the State Water Board determined that the San Francisco v. EPA holding is inapplicable for MS4 permits because the authority to monitor MS4 discharge is based on CWA section 402(p)(3)(B), not 301(b)(1)(C). Additionally, the Board noted that permitting agencies have the discretion to decide if strict compliance with water quality standards is possible, meaning the permitting agencies can decide with which water quality standards the permittee must comply. Finally, the Board found the holding did not affect state law. Under the Porter-Cologne Water Quality Control Act, the State Water Board has separate authority to impose water quality standards, including the use of end-result requirements. The State Water Board found such precedent controlling for MS4 permits, meaning San Francisco may still be required to adhere to end-result requirements after all.
As a result of the Supreme Court ruling and the State Water Board holding, the applicability of these “end results” restrictions will likely depend heavily on the state the NPDES Permit is issued. States could determine that these MS4 NPDES permits are not authorized to include these “end result” provisions. States could also hold that they are permitted to include these “end result” provisions if the authority to issue the NPDES permit comes from CWA authority outside of Section 301; if states take this position, than the citizen suit provisions allowing enforcement of these “end result” provisions would remain. For states like California with their own state version of the CWA, these states could hold that “end result” provisions are still applicable under state law; however, imposing these state law authorized “end result” provisions would prevent enforcement by citizen suits. The ramifications of this case is unknown and it will be interesting to watch how states respond to San Francisco v. EPA.
