City and County of San Francisco vs. EPA: Implications for Clean Water Act Permittees

On March 4, 2025, the U.S. Supreme Court issued its opinion in the case City and County of San Francisco v. Environmental Protection Agency, in which it held that “end-result” requirements routinely imposed by the U.S. Environmental Protection Agency (EPA) in permits were not allowed under the Clean Water Act (CWA). This pivotal opinion has major implications for the manner in which permits under the CWA National Pollutant Discharge Elimination System (NPDES) are administered across the country.

Case Background

The CWA authorizes EPA to implement regulations to ensure that the water quality for receiving water bodies like lakes, rivers, and bays are suitable for their intended use. One tool that the EPA uses is that it issues NPDES permits that set certain limitations on discharges to receiving waters within its jurisdiction.

This particular case dealt with a NPDES permit issued to the City and County of San Francisco (San Francisco) under the CWA for its Oceanside combined wastewater treatment facility. While the NPDES permit contained specific effluent limitations and narrative limitations that San Francisco did not challenge, the dispute in this case centered on two so-called “end-result” provisions found in the NPDES permit:

1. A prohibition against discharges that “contribute to a violation of any applicable water quality standard” for receiving waters.
2. A prohibition against performing any treatments or making any discharges that “create pollution, contamination, or nuisance as defined by California Water Code section 13050.”

Supreme Court Majority Opinion

In the majority opinion delivered by Justice Alito and joined by Justices Roberts, Thomas, Kavanaugh and Gorsuch (Justice Gorsuch joined as to all but Part II of the majority opinion), the Supreme Court held that Section 1311(b)(1)(C) of the CWA does not authorize the EPA to include “end-result” provisions in its NPDES permits. The majority opinion explained that the enforcement responsibility for determining and implementing steps to achieve water quality standards falls within the EPA's mandate and cannot be shifted onto permittees through general outcome-based language.

In reaching this holding, the majority opinion first dismissed an argument made by San Francisco that all “limitations” imposed under Section 1311 of the CWA must qualify as effluent limitations, focusing on the express language of the statute and the consequences of San Francisco’s interpretation of the statute. Notwithstanding the fact that it rejected San Francisco’s primary argument against the “end-result” provisions of the NPDES permit (in which the dissent also joined), the majority opinion went on to address San Francisco’s more narrow argument that Section 1311(b)(1)(C) of the CWA does not authorize EPA to impose requirements that condition permitholders’ compliance on whether receiving waters meet applicable water quality standards. On this latter theory, the majority opinion sided with San Francisco.

The majority opinion held that such “end-result” limitations neither fit the statutory interpretation envisioned by the CWA nor was supported by the legislative history behind the 1972 adoption of the CWA. The majority opinion also examined the broader statutory scheme of the CWA, concluding (1) that “end-result” limitations were inconsistent with the “permit shield” provision of 33 U.S.C. § 1342(k) of the CWA and (2) that such limitations could not reconcile such provisions with “the problem that arises when more than one permittee discharges into a body of water with substandard water quality.”

Based on this analysis, the majority opinion held:

In sum, we hold that §1311(b)(1)(C) does not authorize the EPA to include “end-result” provisions in NPDES permits. Determining what steps a permittee must take to ensure that water quality standards are met is the EPA’s responsibility, and Congress has given it the tools needed to make that determination. If the EPA does what the CWA demands, water quality will not suffer.

Dissenting Opinion

Justice Barrett, along with Justices Sotomayor, Kagan, and Jackson, dissented in part. While the dissent agreed with the majority opinion dismissing San Francisco’s argument that all “limitations” imposed under Section 1311 of the CWA must qualify as effluent limitations, the dissent instead contended more broadly that ‘end-result’ requirements were within the permissible range of limitations necessary to effectively implement EPA’s statutory obligations.

Implications for CWA Permittees and Other Stakeholders

This case addresses a longstanding dispute between EPA and many permittees regarding “end-result” permit requirements frequently found in NPDES permits. It could have major implications for both the EPA and permittees across the country:

• EPA Responsibility in NPDES Permits – The opinion now shifts the responsibility for developing explicit compliance measures onto EPA in crafting NPDES permit requirements rather than allowing the agency to rely on general language for ensuring water quality that previously placed the burden onto permittees.
• Impacts on Processing of NPDES Permits – One area to watch in the wake of the City and County of San Francisco opinion is how the EPA administers and processes NPDES permits, including critical general permits on which many businesses rely. The dissent cautions that if EPA must impose individualized conditions for each permittee under Section 1311(b)(1)(C) of the CWA, then it will “be more difficult and more time consuming for the Agency to issue permits.” It is unclear whether the current Administration’s goal to reduce EPA staffing will further impair such efforts.
• State Regulators – States like California not only have assumed NPDES permitting authority under the CWA, but also have independent discharge permitting authority under state laws (e.g., Porter-Cologne Act). With respect to NPDES permits under the CWA, many states previously had plans to place additional numeric limits in NPDES permits - this opinion may accelerate the implementation of these plans. However, this opinion is limited to implementation of the NPDES permitting program under the CWA, so states with independent discharge permitting authority under state law might continue to use such “end-result” discharge permit conditions pursuant to state law.

Conclusion

The City and County of San Francisco opinion resolves a longstanding issue in the administration of NPDES permits under the CWA, prohibiting the EPA from utilizing so-called “end-result” provisions in such permits. While permittees can now hope for greater clarity on what they must do to comply with permits issued, it will be interesting to see what implications this case has on the EPA’s overall administration of the NPSES permit program.