Supreme Court Decides City and County of San Francisco, California v. Environmental Protection Agency

On March 3, 2025, the U.S. Supreme Court decided City and County of San Francisco, California v. Environmental Protection Agency, No. 23-753, holding that Section 1311(b)(1)(A) of the Clean Water Act does not authorize the EPA to include “end-result” provisions in NPDES permits issued to entities that wish to discharge pollutants into U.S. Waters. “End-result” provisions are permit requirements that make a permittee responsible for the overall water quality in a receiving water.  

The case arose when the city of San Francisco challenged provisions in its National Pollutant Discharge Elimination System (NPDES) permit issued by the EPA that held the city responsible for water quality standards in the Pacific Ocean or the San Francisco Bay. The Clean Water Act (CWA) allows the Environmental Protection Agency (EPA) to issue permits under its NPDES scheme that impose requirements on entities that wish to discharge “pollutants” into U.S. waters. The issue before the Court was whether the CWA authorizes the EPA to issue a permit to San Francisco that conditioned compliance with the permit on whether receiving waters met applicable water quality standards. 

Before issuing a permit regarding the discharge of pollutants, the EPA must ensure that the “discharge will meet” certain statutory requirements, including those outlined under CWA’s § 1311. Section 1311(b)(1)(A) states that the EPA must set “effluent limitations,” which specify the quantities of enumerated pollutants that may be discharged. Section 1311(b)(1)(C) requires the EPA to impose “any more stringent limitation, including those necessary to meet water quality standards, . . . or required to implement any applicable water quality standard.” 

San Francisco claimed that two prohibitions in its permit issued under Section 1311(b)(1)(C) were not authorized by the CWA. One prohibition stated that San Francisco could not make any discharge that “contribute[s] to a violation of any applicable water quality standard” for receiving waters. The other provided that the city could not perform any treatment or make any discharge that “create[s] pollution, contamination, or nuisance” as defined in a section of the California Water Code. The EPA’s Environmental Appeals Board rejected the city’s challenge to the permit. The Ninth Circuit rejected the city’s petition seeking review, concluding that Section 1311(b)(1)(C) authorizes the EPA to impose “any” limitations that seek to uphold water quality standards. Judge Collins of the Ninth Circuit dissented, stating that the CWA “draws an explicit distinction between the ‘limitations’ that the agency must devise and impose on a particular permittee’s discharges” and on the water quality standards themselves.

After granting review, the Supreme Court rejected the city’s contention that “limitations” under § 1311(b)(1)(C) were synonymous with “effluent limitations” under § 1311(b)(1)(A) based on a plain reading of the text, because Congress specifically included the word “effluent” in one provision but not another. The Court agreed, however, with the city’s view that § 1311(b)(1)(C) did not authorize the EPA to impose permit requirements conditioning compliance on whether receiving waters meet applicable water quality standards. The Court reasoned that the text, structure, and pre- and post-enactment context supported this interpretation.

First, the Court started with statutory text. The word “limitation” was defined as a “restriction or restraint imposed from without (as by law[)].” Accordingly, a provision that directs a permittee to do specific things is a limitation. But a provision that “simply tells a permittee that a particular end result must be achieved” is not a “limitation” within the meaning of the CWA. 

Next, the plain meaning of the terms “implement” and “meet” in Section 1311(b)(1)(C) further supported its interpretation. The provision tells the EPA to “implement” water quality standards, i.e., to “‘ensure’ ‘by concrete measures’” that they are fulfilled. It also instructs it to impose limitations that are “necessary to meet” water quality standards, which “is most naturally understood to mean a provision that sets out actions that must be taken to achieve the objective.”

Further, the history of the CWA also supported its holding. The government claimed that a permittee could be held liable if the quality of the water into which it discharges pollutants fails to meet water quality standards. But prior to 1972, federal water pollution control legislation contained a provision that imposed such liability. Post-1972, Congress removed that provision. 

And finally, the “broader statutory scheme” supported the majority’s holding. The “permit shield” provision of the CWA deems a permittee compliant if it follows all terms of its permit. Under the EPA’s reading, even if a permittee complies with its permit’s directives, if the quality of the water in its receiving waters dropped below the applicable water quality levels, a permittee would face adverse consequences. Such a reading was difficult to reconcile with the permit shield provision. 

Justice Alito delivered the opinion of the Court, joined by Chief Justice Roberts, Justice Thomas, and Justice Kavanaugh. Justice Gorsuch joined as to all but Part II of the opinion of the Court, and Justices Sotomayor, Kagan, Barrett and Jackson joined only as to Part II. Justice Barrett filed an opinion dissenting in part, which was joined by Justices Sotomayor, Kagan, and Jackson.