In a case that centered on unusual alliances and unpleasant descriptions of raw sewage being released into San Francisco Bay and the Pacific Ocean during rain storms, the U.S. Supreme Court on Tuesday handed San Francisco a victory in a long-running legal battle with the U.S. Environmental Protection Agency.

Handing down a 5-4 decision, the court narrowed the Clean Water Act, America’s landmark water pollution law, and ruled that the EPA set requirements too broadly in issuing permits for the city’s wastewater treatment plants.

The case is the latest in a series of Supreme Court rulings in recent years to rewrite or weaken major environmental laws.

San Francisco officials cheered the opinion, written by Justice Samuel Alito, saying it would provide more fairness and certainty. Industry groups, including the National Mining Association and the American Petroleum Institute, sided with San Francisco, a city that has long billed itself as an environmental pioneer.

“This is a good-government decision that assures certainty in water quality permitting and that every permittee has predictable, knowable standards to protect water quality,” San Francisco City Attorney David Chiu and San Francisco Public Utilities Commission General Manager Dennis Herrera said in a joint statement.

Environmental groups called the decision the latest rollback of pollution laws by the 6-3 conservative majority on the court, and said it could have widespread effects around California and the nation.

“It will result in more pollution, and less accountability,” said attorney Eric Buescher of San Francisco Baykeeper, an environmental group based in Oakland.

The case focused on sewage.

San Francisco has more than 1,900 miles of sewer mains and laterals. Some are more than 100 years old. The city operates two large wastewater treatment plants that run 24 hours a day.

One, the Oceanside Water Pollution Control Plant, is located between Ocean Beach and Lake Merced, along the Great Highway near the San Francisco Zoo. The other, the Southeast Treatment Plant, is located on the city’s east side, near India Basin about 3 miles south of Oracle Park.

The Oceanside plant treats sewage from homes and businesses and discharges it into the Pacific Ocean. The Southeast plant discharges into San Francisco Bay.

For years, the two plants have operated under permits from the EPA and state officials that are required under the federal Clean Water Act. The permits limit how much pollution wastewater plants around the nation can release into oceans, bays and rivers.

But in 2019, the EPA set conditions on the Oceanside plant that not only limited the specific amounts of pollutants coming out of the plant’s discharge pipe but also required that the waters where it discharged meet more general pollution standards.

The EPA banned the plant from making any discharge that “contributes to a violation of any applicable water quality standard.” It also prevented the plant from creating “pollution, contamination or nuisance” under state water regulations.

The city sued, saying the rules were too vague.

“They might as well have said: Do not violate the Clean Water Act,” Tara Steeley, an attorney for the city, told the court in October.

City officials also said high levels of water pollution near the plants, such as fecal coliform, might have come from other sources

But environmental groups argued the rules would improve water quality.

Last October, at the request of groups such as the Sierra Club and Save the Bay, the San Francisco Board of Supervisors voted to settle the case, over fears that the Supreme Court would use it to weaken water pollution rules nationwide.

In 2023, the Ninth Circuit U.S. Court of Appeals ruled against the city. The city appealed to the Supreme Court. California and 14 other states filed briefs in support of the EPA. Several other large cities with older sewage systems similar to San Francisco’s, like New York and Chicago, sided with San Francisco.

In his ruling Tuesday, Alito wrote that the EPA overreached.

“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,” he wrote.

He was joined by justices Clarence Thomas, John Roberts, Brett Kavanaugh and Neil Gorsuch.

Amy Coney Barrett, a conservative, wrote the dissenting opinion. She was joined by Sonia Sotomayor, Elena Kagan and Ketanji Brown Jackson.

The need for the more general water quality rules, she wrote, “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,'” near Oracle Park.

It was unclear Tuesday how the ruling will affect other wastewater plants around San Francisco Bay. But Buescher of San Francisco Baykeeper expects the ruling will lead to more water pollution nationwide as “other cities and industrial facilities to start to bring these kinds of challenges.”

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