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The decision is the latest in which conservative justices have reined in pollution control efforts.

Justice Samuel Alito wrote for the court that EPA can set specific limits that tell cities and counties what can be discharged. But the agency lacks the authority “to include ‘end-result’ provisions,� Alito wrote, that make cities and counties responsible for maintaining the quality of the water, the Pacific Ocean in this case, into which wastewater is discharged.

“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,� he wrote.

One conservative justice, , joined the court's three liberals in dissent. Limits on discharges sometimes still don't insure water quality standards are met, Barrett wrote.

“The concern that the technology-based effluent limitations may fall short is on display in this case,� Barrett wrote, adding that "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.’�

The case produced an unusual alliance of the liberal northern California city, energy companies and business groups.

The EPA has issued thousands of the permits, known as narrative permits, over several decades, former acting general counsel Kevin Minoli said.

The narrative permits have operated almost as a backstop in case permits that quantify what can be discharged still result in unacceptable water quality, Minoli said.

With the new restrictions imposed by the court, “the question is what comes in place of those limits,� Minoli said.

Alito downplayed the impact of the decision, writing that the agency has “the tools needed� to insure water quality standards are met.