WASHINGTON — The Supreme Court’s conservative majority ruled for San Francisco on Tuesday, limiting the power of environmental regulators to prevent ocean discharges of polluted storm water.

At issue was a regulatory dispute over the permitting standards used by the Environmental Protection Agency.

Storm runoff from coastal cities can pollute bays and the ocean, but city managers argued they should not be held responsible for ocean pollution unless it came from their wastewater treatment plants.

Justice Samuel A. Alito Jr. agreed with San Francisco city and county officials and said an “end result” permit is unfair.

Even a city 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 said in San Francisco vs. EPA.

He said the EPA retains ample authority to prevent water pollution.

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

Justice Amy Coney Barrett dissented, noting that the law authorizes the EPA to enforce “any limitation” need to protect clean water.

The court’s three liberals — Justices Sonia Sotomayor, Elena Kagan and Ketanji Brown Jackson — agreed with her dissent.