The city and county of San Francisco argued that these requirements were unclear and stripped them of “permit shield” protections typically allowed for permit compliance.

EPA and environmental groups countered that the backstop language was added to provide an extra layer of protection for public health without going into details better understood by utilities themselves. 

In its ruling, the court said that the new permit language for wastewater treatment facilities discharging a combination of effluent and stormwater into San Francisco Bay and the Pacific Ocean was overly broad and lacked sufficient specificity—agreeing with San Francisco and a broad cross-section of groups that filed supporting briefs, including the Associated General Contractors of America, American Road and Transportation Builders, National Association of Home Builders and National Association of Clean Water Agencies.

“A permittee could do everything required by all the other permit terms. It could devise a careful plan for protecting water quality, and it could diligently implement that plan,” said Associate Justice Samuel Alito, writing for the majority “But if, in the end, the quality of the water in ... receiving waters dropped below the applicable water quality levels, it would face dire potential consequences.” 

The majority wrote that it is the responsibility of EPA, not a local permittee, to set specific requirements to ensure that waters that receive effluent and other discharges meet water quality standards. “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," the opinion said. “If EPA does its work, our holding should have no adverse effect on water quality.”

But siding with the court's three liberals in a dissent, Justice Amy Coney Barrett said: "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.'"

For more than a decade, EPA and local activist groups have fought to force water utilities in the San Francisco region to reduce sewage and other pollution in local waters. Although the Bayside and Oceanside plants at issue in the case have met requirements of previous NPDES permits, heavy precipitation can cause increased amounts of untreated sewage and stormwater to enter those waters. Concerned that new end-result permit language for the facilities could potentially expose San Francisco to punitive action, the city and county challenged it but were rejected at the appeals court level.

Last May, the U.S. Justice Dept. and the California attorney general filed a civil complaint against the city and county seeking financial penalties and improvements to “remedy San Francisco’s repeated and widespread failures to operate its two combined sewer systems and three sewage treatment plants in compliance with the Clean Water Act and its permits.” 

Response to Ruling

Industry groups applauded the high court ruling. “When Clean Water Act permits are transparent and implementable, utilities can invest public dollars in projects that protect water quality instead of guessing what those projects should be,” said Adam Krantz, CEO of the clean water agency group that filed its supporting brief on behalf of numerous public water utilities. “As the Supreme Court said at the outset of the decision, the language objected to by San Francisco and public clean water utilities around the country is not necessary to protect water quality.”

Brian Turmail, vice president of public affairs and workforce at the Associated General Contractors of America, said backstop requirements “unlawfully make the permittee responsible for water quality.”  Without notice of actions required to ensure permit compliance, EPA “exposed permit holders to unknown risks,” including enforcement, criminal penalties and citizen suits even if permit holders adhered to requirements, he added.

But Sanjay Narayan, an attorney for the Sierra Club’s Environmental Law Program, said the decision “ignores the basic reality of how water bodies and water pollution works, and could stymie” EPA's ability to implement the Clean Water Act, which he called “a bedrock environmental law that has kept water safe for the last 50 years.”

He says requiring EPA to understand specific contaminants and pollutants discharged by any wastewater treatment plant in order to issue an NPDES permit will require more agency resources and time. By removing permit flexibility and the ability to backstop permit-specific provisions, said Narayan, “what you end up with is a much more cumbersome process, one that will take longer, be more expensive and demand more resources.” 

Noting the announced reductions of EPA staff and resources by the Trump administration, delays in permits will be the likely result, he says. “Maybe a really heavily staffed agency could do that, but [with the Trump cuts] we’re going to see greater delays … and delays cost money.”