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Amid Long and Costly Legal Battles, SF Urged to Update Wastewater System, Fix Sewage Discharges

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Houseboats are seen along Mission Creek in San Francisco on May 13, 2024. (Katherine Monahan/KQED)

It’s a clear, sunny day on Mission Creek. Kayakers are paddling by, and people are walking their dogs past the houseboats that line the banks near Oracle Park.

But longtime resident Peter Snider said that, especially after heavy rains, some pretty nasty things go floating downstream.

“Condoms,” Snider said. “Turds, actual turds, come down. Dead fish.”

San Francisco discharges nearly 2 billion gallons of combined stormwater and raw sewage each year into Mission Creek and other points around the shoreline.

And this has been an issue for decades. “When I first moved down here,” Snider said, “it used to be called s**t creek.”

Map from the EPA/Water Board lawsuit, showing Bayside and Oceanside outflow points where San Francisco discharges wastewater.

Legal battles

The resulting public health risks are serious, according to a lawsuit the federal EPA and California Water Board filed against the city in May.

“We’ve seen all kinds of complaints from exposure to raw sewage, including rashes on the skin,” said Sejal Choksi-Chugh, executive director of San Francisco Baykeeper, which is one of the plaintiffs. “Anybody who’s swimming in the bay in that area where the discharge is happening, or kayaking, getting water in their face or breathing the vapors in, can definitely be impacted by bacteria.”

The lawsuit said children, the elderly, pregnant women, and people with weakened immune systems are at greater risk and that San Francisco has not been maintaining or operating its sewer system properly.


“They should want to fix this problem,” Choksi-Chugh said. “But they really have not understood the scope and the magnitude, and they have not addressed it in an effective and efficient way.”

The San Francisco Public Utilities Commission said in a statement that it has been improving its infrastructure and has reduced the average number of spills. Jen Kwart of the City Attorney’s Office called the recent lawsuit “a needlessly costly approach that ignores SFPUC’s longstanding willingness to resolve the regulators’ concerns collaboratively.”

This is not the only active court case over San Francisco’s sewer system. In a separate, related lawsuit, the city sued the federal EPA in 2022, claiming that limits on how much sewage and pollutants it could dump into its surrounding waters were too vague. The 9th U.S. Circuit Court of Appeals ruled against San Francisco (PDF), but the Supreme Court recently agreed to hear the city’s appeal. “We are hopeful the court can bring clarity and stability to this area of law,” Kwart said.

A sign along Mission Creek in San Francisco indicates that the water is unsafe to swim in due to ‘sewer discharges’ and bacteria levels that ‘do not meet California standards for water contact recreation’ from May 13, 2024. (Katherine Monahan/KQED)

The court’s decision could have national repercussions. Eric Buescher, senior attorney with San Francisco Baykeeper, said, “The city has given the Supreme Court an opportunity to further weaken the Clean Water Act.”

So, why these long and costly legal battles? Why doesn’t San Francisco just fix its wastewater infrastructure and quit spilling sewage onto its streets and beaches?

Solutions and delays

Part of the challenge is that the city has a combined sewer system — an older style that runs stormwater and sewage through the same pipes and is prone to overflows during heavy storms. Only about 700 American communities have these systems, and now, like San Francisco, they must change their infrastructure (PDF) to comply with the Clean Water Act.

Christopher Kloss, water permits manager for the EPA, said cities are addressing the problem in three main ways: by separating their systems so that sewage and rainwater will run through different pipes; by building tunnels and tanks to store stormwater until it can be treated; and by engineering green spaces to collect rainwater on the surface and prevent it from going into the sewers.

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“These are some of the more complex engineering projects that they might ever design,” Kloss said. And yet, over 95% of these cities have developed plans, he said, and are building controls now.

“In a lot of cases,” Kloss said, “most of the residents don’t even know what’s happening because they’re able to do it in places that are underground, or they’re installing parks and green spaces that folks don’t necessarily recognize are part of the wastewater management system.”

San Francisco said in a statement (PDF) that the kind of upgrade Kloss is talking about would cost residents well over $10 billion. Instead, the city proposes about $2.5 billion in smaller projects that would improve water quality but wouldn’t eradicate sewage discharges completely.

Kloss said there is significant federal funding available through the Bipartisan Infrastructure Act and that the issue is becoming more urgent.

“What we anticipate with climate,” Kloss said, “is not only more rain but more intense downpours. So that will strain these systems even more.”

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