SCOTUS Rules Against EPA in Clean Water Case

In City and County of San Francisco v. EPA, 604 U.S. ____ (2025), the U.S. Supreme Court again limited the Environmental Protection Agency’s (EPA) power under the Clean Water Act (CWA). According to the Court’s five-member majority, the EPA can’t enforce requirements in wastewater permits that “do not spell out what a permittee must do or refrain from doing.”

Facts of the Case

Under CWA, the EPA and authorized state agencies issue permits that impose requirements on entities that want to discharge “pollutants” into the waters of the United States. The National Pollutant Discharge Elimination System (NPDES) makes it unlawful to discharge pollutants into covered bodies of water unless authorized by permit. These permits typically include “effluent limitations” on discharges that restrict the “quantities, rates, and concentrations of chemical, physical, biological, and other constituents.” Failure to comply with permit limitations exposes permit tees to civil penalties and even criminal prosecution. Under what is known as the “permit shield” provision, however, an entity that adheres to the terms of its permit is deemed to be compliant with the CWA.

The case before the Court involves a challenge to “end-result” requirements—permit

provisions that do not spell out what a permittee must do or refrain from doing but instead make a permittee responsible for the quality of the water in the body of water into which the permittee discharges pollutants. The City of San Francisco operates two combined wastewater treatment facilities that process both wastewater and stormwater. During periods of heavy precipitation, the combination of wastewater and stormwater may exceed the facility’s capacity, which can result in the discharge of untreated water, including raw sewage, into the Pacific Ocean or the San Francisco Bay.

In 1994, the EPA adopted its CSO Control Policy, which requires municipalities with combined systems to take prescribed measures and to develop and implement a Long-Term Control Plan, and provides for a two-phase permitting process. For many years, San Francisco’s NPDES permit for its Oceanside facility was renewed without controversy. However, in 2019, the EPA issued a renewal permit that added two end-result requirements. One prohibits the facility from making any discharge that “contribute[s] to a violation of any applicable water quality standard” for receiving waters, while the other provides that the City cannot perform any treatment or make any discharge that “create[s] pollution, contamination, or nuisance as defined by California Water Code section 13050.”

San Francisco argued that the end-result requirements exceed EPA’s statutory authority. However, the Ninth Circuit Court of Appeals denied the city’s petition for review. It held that §1311(b)(1)(C) authorizes EPA to impose “any” limitations ensuring applicable water quality standards are satisfied in a receiving body of water.

Supreme Court’s Decision

The Supreme Court reversed by a vote of 5-4. It held that Section 1311(b)(1)(C) does not authorize the EPA to include “end-result” provisions in NPDES permits.

“We hold that the two challenged provisions exceed the EPA’s authority. The text and structure of the CWA, as well as the history of federal water pollution legislation, make this clear. And resorting to such requirements is not necessary to protect water quality,” Justice Samuel Alito wrote. “The EPA may itself determine what a facility should do to protect water quality, and the Agency has ample tools to obtain whatever information it needs to make that determination. If the EPA does its work, our holding should have no adverse effect on water quality.”

In reaching its decision, the Court emphasized that the “end-result” limitations do not fit the statutory interpretation envisioned by the CWA. In support, it cited that the pre-1972 Water Pollution Control Act (WPCA) contained a provision that allowed direct enforcement against a polluter if the quality of the water into which the polluter discharges pollutants failed to meet water quality standards, which was expressly omitted when Congress overhauled the law.

The Supreme Court went on to find that two features of the broader statutory scheme further support its conclusion. First, end-result requirements would negate the CWA’s “permit shield” protecting compliant permittees from liability. Second, EPA’s interpretation provides no mechanism for fairly allocating responsibility among multiple dischargers contributing to water quality violations. “When a permit contains such requirements, a permittee that punctiliously follows every specific requirement in its permit may nevertheless face crushing penalties if the quality of the water in its receiving waters falls below the applicable standards,” Justice Alito wrote.