Supreme Court Puts Another Limit on the EPA’s Ability to Protect Water

As the Trump administration slashes the agency’s budget, the court’s conservative majority sided with San Francisco and industry groups to limit EPA enforcement of Clean Water Act permits.

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A view of Baker Beach on the shores of the Pacific Ocean in San Francisco on Feb. 26. Credit: Tayfun Coskun/Anadolu via Getty Images
A view of Baker Beach on the shores of the Pacific Ocean in San Francisco on Feb. 26. Credit: Tayfun Coskun/Anadolu via Getty Images

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In a case that saw an iconic liberal city team up with industry to challenge regulations from the U.S. Environmental Protection Agency, the Supreme Court today once again limited the agency’s power to regulate the environment by siding with a coalition San Francisco formed with fossil fuel, mining and agricultural groups.

The court’s conservative majority ruled in favor of the city, the National Mining Association, American Farm Bureau Federation and American Fuel and Petrochemical Manufacturers in a 5-4 vote over how the EPA prohibits and penalizes pollution under the 1972 Clean Water Act.

Under the law, the EPA could hold those it granted permits for discharging pollution into U.S. waters broadly responsible for the quality where they do so; in San Francisco’s case, the EPA had included in its permit a provision that said a city-run wastewater facility could not cause or contribute to a violation of water quality standards in the Pacific Ocean, but did not specify how the city should comply.

All but one of the court’s six conservative justices decided that type of provision was not permissible under the Clean Water Act. Writing for the majority, Justice Samuel Alito said broad language holding San Francisco responsible for pollution “exceed the EPA’s authority,” adding that “resorting to such requirements is not necessary to protect water quality.”

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“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,” he continued. “If the EPA does its work, our holding should have no adverse effect on water quality.”

The Trump administration has broadcast its goal of reducing the EPA’s budget by 65 percent, a drastic cut motivated by the administration’s belief that the agency has “fulfilled its mission,” according to reporting by the New York Times. 

Environmental law experts worry the EPA, facing potentially billions in lost funding and a shrinking federal workforce under the Trump administration, would be in no position to undertake the kind of work necessary to keep polluters in check.

“We’re going to end up in a situation where we either have very long delays to get these permits written or we’re just going to have permits that aren’t strong enough and they don’t include limits on all the different contaminants in the discharge,” said Becky Hammer, a senior attorney for the Natural Resources Defense Council. “We’re going to have worse water quality across the country. It’s really not a good outcome.”

In order for the EPA to administer permits as Justice Alito envisions and still protect water quality, “it’ll need to know everything about what might be discharged before a clean-water permit can be issued—making the permitting process delayed and incredibly expensive,” said Sanjay Narayan, chief appellate counsel of Sierra Club’s environmental law program, in a statement.

“The result is likely to be a new system where the public is regularly subjected to unsafe water quality.”

Without language holding polluters broadly accountable, “it could work out to the benefit of a lot of polluters,” Hammer said, which is why outside groups joined the case, which made the leap to the Supreme Court after a ruling in favor of the EPA from the Ninth Circuit Court of Appeals in 2023. 

“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,” said Ashley Burke, senior vice president of communications for the National Mining Association. “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,” she said.

The EPA and the American Farm Bureau Federation said they were reviewing the decision. American Fuel and Petrochemical Manufacturers did not immediately return requests for comment.

San Francisco argued the provisions exposed it to lawsuits even when it followed its permits. “We are very pleased the Court issued the narrow decision San Francisco sought,” the city said in a statement posted on the city attorney’s website. “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.” 

The dissenting opinion authored by Justice Amy Coney Barrett, which also represented the stance of the court’s three liberal justices, questioned the court’s reading of the agency’s authority and its need to specify how pollution should be avoided. “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 [it] serves to safeguard?” the justice wrote. 

Less than two years ago, in Sackett vs. EPA, the Supreme Court issued a ruling weakening protections for wetlands and streams. Today’s ruling appears to make water pollution more difficult for the agency to address.

“This really just seems like part of a pattern or a concerted effort by the court to chip away at our tools to keep our environment safe and healthy,” Hammer said.

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