San Francisco City Attorney David Chiu pushed back on the criticism, arguing the permits don’t limit the number of discharges that can take place in a year. “This case was never about challenging or seeking any change to the Clean Water Act, nor disputing EPA’s ability to enforce environmental protections,” Chiu said in a statement. “I am confident we made the right choice to protect San Franciscans.”
The SFPUC argues that the exact amount of sewage that ends up in waterways varies based on each storm, and some of the pollution could come from other sources. Officials maintain that only a small percentage — less than 10% — of water discharged during storms is partially treated sewage. Most of the year, the system dispenses clean water, they say.
“I liken it to drinking a martini,” said Joel Prather, the SFPUC’s assistant general manager for wastewater enterprise. “I’m drinking the mixture of whatever alcohol I choose and the vermouth. And so, by the same token, there is a mix in there, but it’s designed to settle the solids out. And as it’s being discharged, it is primarily stormwater being discharged.”
‘The problem has definitely grown worse’
During last week’s storms, at least 20 sites discharged polluted water near Ocean Beach, Crissy Field, the Financial District, Mission Creek and Hunters Point, according to the SFPUC’s beach water quality map.
SF Baykeeper captured images of dirty water containing fecal matter and trash overflowing into Mission Creek on Feb. 4.
Choksi-Chugh said these areas are “sacrifice zones” where the city has nowhere else to release polluted water.
“The problem has definitely grown worse,” she said. “They’re not allowed to be discharging this much bacteria and pollution into the bay, yet they are doing it.”
The issue is deepening because storms are often more intense than they used to be and can easily overwhelm the system first established more than a century ago. Scientists predict storms could become up to 37% wetter by the end of the century.
“We are seeing significant storms, and we’re not alone here; the entire world is seeing stronger storms and having to deal with them,” Prather said. “We’re a combined system, so it’s designed to discharge before it floods on the street. But these large storms are overcoming everything.”
Entirely revamping the city’s aging sewage and stormwater infrastructure would cost San Francisco ratepayers well over $10 billion on the bayside alone, which “would require major increases to wastewater bills,” according to the SFPUC.
Drew Madsen, the head of Blue Water Task Force, a volunteer-run water quality testing program, holds water samples taken from India Basin at the Surfrider Foundation’s lab in San Francisco’s Outer Sunset neighborhood on Thursday, Feb. 6, 2025. The samples are mixed with a reagent, which gives them a yellow color and reacts with bacteria, causing the samples to glow under UV light. (Beth LaBerge/KQED)
Chicago significantly reduced its discharges by digging giant tunnels underground to catch stormwater in the days after a storm. However, Prather said digging under densely populated San Francisco is unrealistic and would not pencil out.
“You’re talking tens of billions of dollars. You’re also talking about ripping up every street in San Francisco and putting new plumbing in,” he said.
San Francisco has invested $2 billion to reduce discharges by 80% of the 7.6 billion gallons it released annually half a century ago, Prather said. The agency has planned for nearly $4.9 billion in wastewater projects in its 10-year capital plan, approved in 2023, including sewer system improvements, treatment facility updates and a Treasure Island treatment plant.
‘Best we can with the resources we have’
“At the end of the day, it’s just doing the best we can with the resources we have right now to be prepared for those storms,” he said.
During regular rain storms, the city collects rainwater at its two plants. Collection boxes can hold 200 million gallons of water before spilling. The agency aims to capture a billion gallons of stormwater annually using green infrastructure by 2050.
“Rainwater or street runoff hits the green infrastructure and percolates into the ground before going on to either groundwater or our treatment facilities,” Prather said.
The agency also offers a grant program for residents experiencing flooding on their properties.
“We’re not sitting on our hands doing nothing,” he said.
Sedlak, of UC Berkeley, said San Francisco needs to prioritize its combined sewer overflow problem. “At this point, I’m not seeing the combined sewer overflow challenge as their highest priority,” he said.
He added that storms would only worsen with human-caused climate change, making hydroclimate whiplash — fast swings between alarmingly wet and seriously dry weather — more intense, and said San Francisco would have to make some sort of compromise.
