Supreme Court strikes down EPA rules on discharge of water pollution

by Justin Jouvenal, Maxine Joselow (c) 2025 , The Washington Post

The Supreme Court on Tuesday struck down rules regulating the discharge of water pollution, narrowing the landmark Clean Water Act in an unusual case that pitted one of the nation’s greenest cities – San Francisco – against the Environmental Protection Agency.

In a 5-4 ruling, the justices found that the EPA cannot impose generic prohibitions against violating water quality standards. The ruling could affect businesses and other cities that sit on bodies of water, including New York, Boston and Washington.

San Francisco sued the EPA after the agency found the city in violation of the terms of a 2019 permit required to discharge pollution from its wastewater system into the Pacific Ocean.

City officials argued that the EPA had exceeded its authority because the permit rules were so vague that it was impossible to know when they had crossed a line.

San Francisco’s wastewater permit includes 100 pages of detailed rules on effluent limits. But the city objected to additional, less specific standards that hold officials responsible for discharge that contributes to a violation “of any applicable water quality standard.”

During oral arguments in October, the Biden administration said the generic rules are an important backstop to the specific limits it imposes on water pollution. Officials also said they would like to impose more specific limits, but the EPA has been hampered by a lack of information from the city about its discharge. San Francisco denies that claim.

The justices rejected the EPA’s argument.

“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 Samuel A. Alito Jr. wrote in the majority opinion.

San Francisco has an aging treatment plant that combines stormwater and sewage. It can overflow during heavy rains, sending household waste, including fecal water, into outfalls in the Pacific Ocean. The facility serves about 250,000 residents and 250 miles of sewers.

San Francisco said in court that it has spent billions to upgrade the facility to try to meet pollution benchmarks. It is already facing at least $313 million in fines from a similar issue with a wastewater facility that empties into the San Francisco Bay. The city said in that case that it would cost a whopping $10.6 billion to bring that facility into compliance.

The case had divided environmental groups that are often aligned with both the EPA and liberal cities such as San Francisco in court. Some had voiced concerns that the Supreme Court’s 6-3 conservative majority would use the case to weaken clean-water regulations nationwide, going even further than San Francisco had requested.

“This decision is going to make the job of EPA and other permitting agencies much harder, because the type of limits the court says have to be used are much harder to identify and calculate,” said Becky Hammer, a senior attorney at the Natural Resources Defense Council.

Sam Sankar, senior vice president for programs at the environmental law firm Earthjustice, criticized the justices for adding to the EPA’s workload as the Trump administration slashes the agency’s staffing and spending levels. President Donald Trump said last week that EPA Administrator Lee Zeldin was considering cutting 65 percent of the agency’s workforce, although the White House later clarified that the president was referring to a 65 percent cut in the agency’s overall budget.

“The majority is saying EPA can still protect water quality if it invests more staff time in issuing each permit,” Sankar said. “I guess they haven’t heard that Trump is gutting the agency.”

The case featured some other strange bedfellows, with San Francisco drawing support from several business trade groups, including the U.S. Chamber of Commerce, the National Mining Association and the National Association of Homebuilders.

“Today’s ruling restores the proper limits to EPA’s authority and returns certainty to responsible businesses seeking to adhere to the requirements of their permits,” Conor Bernstein, a spokesman for the National Mining Association, said in an email. “This return to the text and intent of the Clean Water Act eliminates the widespread regulatory uncertainty and litigation risk presented by the flawed Ninth Circuit decision.”

San Francisco petitioned the Supreme Court to take up the case after the U.S. Court of Appeals for the 9th Circuit sided with the EPA.

Justice Amy Coney Barrett and the court’s three liberal justices dissented in part from Tuesday’s ruling, arguing that the EPA had the authority to impose generic prohibitions under the terms of the Clean Water Act.

“The concern that the technology-based effluent limitations may fall short is on display in this case – discharges from components of San Francisco’s sewer system have allegedly led to serious breaches of the water quality standards, such as ‘discoloration, scum, and floating material, including toilet paper, in Mission Creek,’” Barrett wrote, citing the EPA’s case against San Francisco.

The decision is the latest by the high court to curtail the EPA’s ability to regulate pollution. Last summer, the justices temporarily blocked a major agency initiative to regulate air pollution that drifts across state lines. That litigation is continuing to play out in the lower courts.

In 2o22 and 2023, the justices limited the agency’s ability to tackle climate change and protect wetlands from runoff.

San Francisco Supervisor Myrna Melgar blasted the city Tuesday for bringing the case against the EPA.

“It is deeply troubling to see San Francisco, a city known for its environmental leadership, play a significant role in weakening the very protections that safeguard our water and natural resources,” she said in a statement. “This decision aligns with President Trump’s broader rollback of environmental regulations.”