After an unprecedented harmful algae bloom first turned San Francisco Bay a murky brown color and then littered its shores with dead fish, many people assumed it was yet another climate disaster to add to the list, along with extreme drought, wildfires and heat waves.

While scientists suspect climate change played a role in triggering the bloom, what fueled it is not a mystery. Algae blooms need food to grow, and this one had plenty: nutrients originating in wastewater that the region’s 37 sewage plants pump into the bay.

In other words — we wouldn’t have this problem without the poop and pee of the Bay Area’s 8 million residents.

Birds float on an algal bloom in Berkeley, Calif., Wednesday, Aug. 31, 2022. Thousands of fish have washed ashore all over the Bay Area due to a harmful algal bloom. The microorganism, Heterosigma akashiwo, is believed to be the largest harmful algal bloom seen in the region in over a decade.

An algal bloom at Lake Merritt in Oakland, Calif., Wednesday, Aug. 31, 2022. Thousands of dead fish washed ashore at Lake Merritt due to a harmful algal bloom spreading across the Bay Area. The microorganism, Heterosigma akashiwo, is believed to be the largest harmful algal bloom seen in the region in over a decade.

“For those of you who aren’t aware, when you flush the toilet every day, you’re flushing nutrients down,” Eileen White, executive officer of San Francisco Bay Regional Water Quality Control Board, said at a news conference last week. The waste arrives at the sewage plant and is treated, she explained, but those nutrients — mostly nitrogen and phosphorous — remain in the water that is discharged into the bay.

There has been no evidence of a raw sewage leak; rather, it’s the regular amount of those nutrients that have long made the bay primed for a harmful algae bloom like this one, which started in late July in Alameda and has recently flared up as far as Sausalito, Vallejo and Fremont.

Nutrients “may not have triggered this specific event,” said David Senn, senior scientist at SF Bay Nutrient Management Strategy of the San Francisco Estuary Institute, a group formed to study the issue 10 years ago. “But they contributed to its size, the amount of the organism and how long it lasted.”

The regional water board has told agencies that it will probably require caps on nutrients in wastewater when their regional permit comes up for renewal in 2024. But upgrading dozens of aging treatment facilities could cost $14 billion, which would double or triple ratepayers’ water bills, White said in an interview.

“It’s a multibillion-dollar Bay Area issue that needs to be thought through very carefully, taking the science into effect,” she said. “There’s all of sorts of different treatments, and none of them are cheap.”

A major challenge is that most of the treatment plants date to the 1970s and ’80s, after the passage of the 1972 Clean Water Act and other regulations. Previously, municipalities simply pumped raw sewage into the bay.

Federal, state and local governments and the treatment plants themselves have spent millions to research the issue, but like much of climate change planning, the science and policy are moving slower than the problem is progressing.

Grease and scum float in a raw sewage intake tank at the San José-Santa Clara Regional Wastewater Facility on Thursday, Sept. 1, 2022, in San Jose, Calif.

A dead bat ray is surrounded by other dead fish at Lake Merritt in Oakland, Calif., Wednesday, Aug. 31, 2022. Thousands of dead fish washed ashore at Lake Merritt due to a harmful algal bloom spreading across the Bay Area. The microorganism, Heterosigma akashiwo, is believed to be the largest harmful algal bloom seen in the region in over a decade.

“There has been planning going on, but there is a reluctance to face the facts that something needs to be done soon,” said Ian Wren, staff scientist at the environmental group SF Baykeeper. “But I think as the science does mature over the next couple years, we’re going to get there. This event will surely open some eyes about the need to do something.”

The algae bloom, of an organism called Heterosigma akashiwo, is most toxic to fish, requiring an emergency cleanup of dead fish at Lake Merritt. In the bay it has killed a reported 10,000 yellowfin goby along with hundreds of striped bass and white sturgeon and a small number of endangered green sturgeon, according to the state Department of Fish and Wildlife. Though the bloom was showing signs of slowing down this week, the heat wave may exacerbate it.

“If loads from wastewater treatment plants had been lower, would that have prevented this event or lessened its extent?” said Lorien Fono, director of Bay Area Clean Water Agencies, which represents the 37 plants and said they’re waiting on research to determine that. “This is not something we’ve seen before.”

Some local agencies have taken steps to reduce their nutrient loads, while others have been less proactive. The San Jose/Santa Clara Regional Wastewater Facility, which serves Silicon Valley, releases more discharge water into the bay than other large facilities, at an average of 85 million gallons per day. Yet its nitrogen load is 5.5 tons a day.

Meanwhile San Francisco’s treatment plants release an average of 55 million gallons of wastewater into the bay daily, with 9.5 tons of nitrogen; the city also releases additional wastewater into the ocean.

“There are many of us who discharge into our San Francisco Bay Estuary, but we are certainly one of them,” said San Francisco Supervisor Aaron Peskin, who plans to conduct a hearing on the issue this month. “We’ve got a ways to go not just on the bay side, but also on the ocean side,” he said, when it comes to reducing the nutrient load in effluent.

But he noted that the SFPUC is funded by ratepayers, who need to be taken into account.

“The issue of bellying up to the bar and spending hundreds of millions of dollars to deal with what climate change is going to require us to do, to reduce our nitrogen loads, is not going to happen overnight,” he said.

John Coté, spokesperson for the SFPUC, said in a statement that the agency is an active participant in the scientific studies on nutrients in the bay.

“We are currently in compliance with all of our regulatory requirements, and we stand ready to undertake the planning and implementation around any modified nutrient-based regulatory requirements that the Regional Water Quality Control Board issues in the future,” he said.

Algae need the same things that crops need to grow — sunlight, nitrogen and phosphorous. While the nitrogen and phosphorus have long been in the water due to the treatment plants, the sunlight has been hampered by frequent fog or wind that stirs up sediment, making it less clear, or more turbid.

Crews remove dead fish from Lake Merritt in Oakland in August. Thousands of dead fish washed ashore at Lake Merritt because of a harmful algae bloom spreading across the Bay Area. The microorganism, Heterosigma akashiwo, is believed to be the largest harmful algae bloom seen in the region in over a decade.

Scientists have expected changing weather patterns from global warming would turn on the switch to make the various types of algae that are ever present in the bay bloom. The wind and fog could die down, and more frequent and severe heat waves could heat up the water, promoting more growth.

The water in the bay has also been more clear in the past decade, likely because the heavy sediment that originally made it down from the Sierra during the Gold Rush has finally stopped flowing into rivers for the most part, said Warner Chabot of the San Francisco Estuary Institute.

Bay Area residents’ role in the issue starts with the flush of the toilet — each of us contributes 0.03 pounds of nitrogen per day, White said. The waste goes to wastewater treatment plants and through various processes including chlorination and dechlorination, removing pathogens, before it’s pumped into the bay. And while this water is generally safe for marine life, it’s not often given an extra step and filtered for nutrients that algae needs to grow and bloom.

Thousands of fish like this sturgeon on Mare Island have washed up on bay shores because of a harmful algal bloom.

San Jose/Santa Clara Regional Wastewater Facility is among the local agencies that do take that extra step, sending the treated water through a series of four tanks that encourage the growth of bacteria that remove nitrogen from the water.

“The science is still premature in determining the exact cause of these algal blooms, but we’re going to continue to do what we can on our part,” said Amit Mutsuddy, deputy director of the facility.

In the past year, the amount of nitrogen in its effluent went down from 17 to 11 milligrams per liter at no extra cost, just by using existing infrastructure, he said.

But other agencies may have to spend up to $1 billion, depending on where treatment facilities are located, White said.

Other ways to deal with nutrients include recycling wastewater and constructed wetlands, a nature-based process that uses soil and vegetation to treat water, but those processes are still being evaluated for their cost-effectiveness.

“We’re all in this together. We’re all going to have to pay for this,” Wren said. “If you’re OK with that, we’re going to have a better bay.”

Thousands of dead fish washed ashore at Lake Merritt due to a harmful algal bloom spreading across the Bay Area.

Tara Duggan is a San Francisco Chronicle staff writer. Email: tduggan@sfchronicle.com Twitter: @taraduggan

Tara Duggan is a staff writer in The Chronicle's climate and environment team who focuses on the ocean, fisheries, food and agriculture. Previously in the Food+Wine department, where she earned a James Beard Foundation Award and other accolades, Tara is also the author of several cookbooks, including "Steamed: A Catharsis Cookbook," "Root to Stalk Cooking" and "The Working Cook." Her articles and recipes have appeared in the New York Times, Food & Wine Magazine and the Wall Street Journal.