High Court Rejects EPA Sewage Permits in San Francisco Win (3)

The US Supreme Court on Tuesday rejected EPA “end result” sewage permits issued under the Clean Water Act that focus on water quality instead of outlining specific requirements to prevent pollution.

In a fractured 5-4 ruling written by Justice Samuel Alito, the court blocked the EPA from issuing permits that make a permittee responsible for surface water quality, or “end result” permits—a term the court coined in the ruling. National Pollution Discharge Elimination System permits govern pollution from sewer overflows during storms.

Determining specific steps a permittee must take to meet water quality standards are the EPA’s responsibility, the court ruled.

The ruling is a partial win for San Francisco, which challenged nonspecific, or “narrative,” wastewater permits the Environmental Protection Agency issues to protect surface water quality. The city wanted the EPA to specify measures it needed to take to prevent its sewage overflow system from polluting the Pacific Ocean, but the EPA issued only narrative permits.

Chief Justice John Roberts and Justices Clarence Thomas and Brett Kavanaugh joined Alito, along with Justice Neil Gorsuch, who joined part of the majority opinion. Justices Amy Coney Barrett, Elena Kagan, Sonia Sotomayor, and Ketanji Brown Jackson dissented in part.

Environmental lawyers disagree on the impact of the ruling. Kevin Minoli, partner at Alston & Bird LLP in Washington, said the ruling upends the EPA’s 50 year-old approach to writing NPDES permits, and it’s unclear what will replace the agency’s narrative permit limitations.

But the ruling “is not a blockbuster decision,” and it will have a minimal impact on San Francisco’s water system, said Dave Owen, an environmental law professor at the University of California College of the Law in San Francisco. Two paragraphs in the city’s NPDES permit will need to be changed, and much of the rest of it will remain unchanged, he said.

More broadly, “a lot of permits will now need to be rewritten, which is a big hassle for everyone involved,” he said. “The impact on water quality is harder to assess.”

End Result Permits

The case involves provisions of the Clean Water Act that don’t spell out what a permittee must do to uphold water quality standards. Instead, they make a permittee directly responsible for water quality, Alito wrote.

When a permit contains such requirements, a permittee such as San Francisco that follows every specific requirement “may nevertheless face crushing penalties if the quality of the water in its receiving waters falls below the applicable standards,” he wrote.

“End result” permits exceed the Clean Water Act’s authority, the court ruled.

The EPA said Tuesday it’s reviewing the decision.

San Francisco City Attorney David Chiu and Public Utilities Commission General Manager Dennis Herrera said in a statement the court issued a narrow ruling that makes it clear permit holders are responsible for their waste discharges.

“But it’s not lawful to punish permit holders for things outside of their control, such as the end-result water quality of a shared body of water, where many other factors affect water quality,” Chiu and Herrera said.

The ruling is a partial win for San Francisco. The court rejected the city’s primary argument that all “limitations” imposed under the Clean Water Act must qualify as effluent, or sewage, limitations. Congress omitted “effluent” from the section of the statute the city was contesting, Alito wrote.

Narrative provisions in permits are common, but they don’t directly restrict specific quantities of pollutants, and San Francisco acknowledged such permits are legitimate, Alito wrote.

However, the court supported San Francisco’s alternative argument that the Clean Water Act doesn’t authorize EPA to impose permit requirements that condition a permit holder’s compliance on whether the waters being polluted meet certain water quality standards.

That’s because a polluter could take all actions required to prevent water pollution under its permit and the quality of the waters being polluted could still exceed allowable standards in part because there could be other sources of pollution in the same water. A permittee in that scenario would be subject to penalties despite doing everything in its power to prevent pollution, the court ruled.

The EPA argued it shouldn’t bear the burden of determining what San Francisco should do to uphold water quality standards. The court rejected that argument, which was advanced by the Biden administration.

“It appears that the EPA and state permitting authorities have used end-result requirements routinely, not just when a permit holder has failed to provide necessary information,” Alito wrote. “The EPA possesses the expertise (which it regularly touts in litigation) and the resources necessary to determine what a permittee should do.”

Downplaying Water Quality Controls

In her dissent, Barrett wrote the court invented a new theory that the CWA doesn’t authorize the EPA to direct permittees to comply with water quality standards.

The “entire function” of the relevant section of the CWA “is to ensure that permitted discharges do not violate state water quality standards,” she wrote.

“The provision gives EPA broad authority to achieve that aim through conditions imposed in NPDES permits,” she wrote. “Why would that broad authority not allow EPA to tell permittees that they must not cause or contribute to a violation of the very standards that §1311(b)(1)(C) serves to safeguard?”

The court’s ruling downplays the value of controlling water quality at the receiving end of the pollution because EPA imposes such controls only when it doesn’t have enough information necessary to develop more specific methods, Barrett wrote.

“That is the case here: San Francisco has consistently failed to update its Long-Term Control Plan for managing combined sewer overflows,” she wrote, adding that by imposing receiving-water limitations, EPA was able to issue San Francisco an NPDES permit without additional information.

“The court does not explain what other course of action EPA could take,” Barrett wrote. “Instead, it states, without citation, that ‘EPA possesses the expertise . . . and the resources necessary to determine what a permittee should do.’”

The EPA has been trying to halt San Francisco’s releases of raw sewage into the Pacific Ocean during rainstorms for years, and a lack of information about the cause forced the agency to include generic prohibitions on the impacts to water quality in the city’s permit. The US Court of Appeals for the Ninth Circuit in July 2023 upheld EPA’s authority to issue generic limits on discharges under the Clean Water Act.

San Francisco expected EPA to force it to pay $10 billion in “crushing” penalties for permit violations, Tara Steeley, deputy city attorney for San Francisco, said in oral arguments in October.

The case is the first to grapple with Clean Water Act regulations since the justices struck down Chevron deference in Loper Bright Enterprises v. Raimondo in June 2024, but that issue was barely mentioned during oral arguments.

The case is City and County of San Francisco v. EPA, U.S., No. 23-753, 3/4/25.