It was late July when San Francisco Bay Area residents first grew concerned: the water in a channel near Oakland was turning a murky, tea-colored brown.

Scientists in the region tested the water and found a bloom of algae, Heterosigma akashiwo, that causes a form of what is known as "red tide." By the end of the August, the bloom had spread throughout the San Francisco Bay. Observers who flew over the bay saw that most of the water had turned a reddish brown. And then came the fish kills: dead sharks, sturgeon, stiped bass, minnows, and other sea life washed up and covered local shores.

The algae bloom was the worst in the San Francisco Bay in almost two decades.

Warm water is typically one of the key ingredients algae blooms need to grow, so many people likely assumed that scientists, environmental activists, and mainstream media outlets would point at climate change as the primary cause of the San Francisco Bay bloom. But that's not the case. In a report earlier this month, the San Francisco Chronicle confirmed that what fueled the bloom was not a mystery, and it wasn't the warm weather. Rather, the bloom was fueled by excessive nutrients in the wastewater, or effluent, pumped into the bay by the region's 37 sewage plants.

"Either you're treating the effluent to standards that are safe for the receiving waters or you're not. It doesn't have anything to do with the climate. Either you have working infrastructure or you don't. You're either overflowing raw sewage or you aren't," said Kristi Diener, a California clean water advocate, who is also an advocate for the state's farmers and ranchers.

Diener said the algae bloom and the fish kills, which have since dissipated, caused the Bay Area's eight million residents and its leaders to wake up to the long-brewing problem. San Francisco Bay has among the highest nutrient levels of any bay or estuary in the world.

"The irony is this is happening in the epicenter of supposed environmentalism," she said.

This summer's bloom highlighted a problem that state and local leaders have been aware of for decades: Bay Area wastewater treatment plants, like many similar plants nationwide, treat sewage at a high enough level to prevent direct public health problems, but the wastewater they pump into the bay still contains high levels of nutrients – nitrogen and phosphorus – that feed algae and fuel blooms. Fixing the problem will be expensive, likely costing tens of billions of dollars, but clean water advocates across the political spectrum told National Review that converting sewage plants to treat the region's wastewater at a higher level is critical for the health of the San Francisco Bay and for the Bay Area economy.

Jon Rosenfield, a senior scientist with San Francisco Baykeeper, an environmental advocacy organization, said conditions for toxic algae blooms have long existed in San Francisco Bay, and they could become more common as nutrient levels increase and temperatures warm. Those blooms are a threat to local tourism and regional fisheries, and could make it harder for local businesses to grow and attract workers, he said. Rosenfield called San Francisco Bay the "unappreciated heart of the Bay Area's economy."

"If it's turning red and killing things and maybe becomes toxic to people for a few weeks out of every year, that is not going to be good for the Bay Area," he said.

This is not just a San Francisco Bay problem. Algae blooms have become more common, longer lasting, and increasingly toxic across the U.S. and elsewhere. This summer, California's state water agency issued a danger advisory over a blue-green algae bloom in the San Luis Reservoir in central California, urging people not to swim in the water or eat fish from the lake. Algae blooms have become more common in the Great Lakes, and even in Lake Superior, where summer water temperatures typically hover around 60 degrees. In 2018, an explosion of blue-green algae and red tide across much of Florida fouled local waters, drove tourists away, and devastated local economies.

"It's a growing problem, and it's becoming a bigger issue in both beachfront communities, as well as lake and river communities," said Darcy Burke, a business consultant and Southern California water district president, adding that algae is a natural part of the ecosystem, and generally "it's not a bad thing."

"What happens, though, and it's happening more and more as water bodies get more shallow and warmer, and there's more nutrients added to the water, you have algae blooms that kind of take over," she said.

Nutrients flowing into San Francisco Bay come from a variety of sources. Urban stormwater runoff that includes fertilizers and pet waste contributes to the problem. Diener expressed concerns about regular sewage leaks from broken and outdated sewer pipes.

Agricultural runoff accounts for 15 percent to 20 percent of the nutrients in the bay, though it varies by location and time of year. "Farms do contribute," Burke said, but "because water's such a scarce resource, farmers do everything they can to avoid runoff."

Burke also pointed to the impact of the large homeless population in the Bay Area. "When you have the amount of homeless that Los Angeles and San Francisco have, and people are defecating in the street, and that defecation goes right into the stormwater system, which goes right into the bay, it adds to the problem," she said. "That's not treated at all."

But Rosenfield said there's no doubt that the biggest source of nutrients flowing into the San Francisco Bay is the region's wastewater plants – they're responsible for over 60 percent. In addition to cleaning out biosolids, Bay Area wastewater plants use processes that are designed to kill bacteria dangerous to humans, and remove some – but not all, and not enough – of the nutrients and salts in the water.

"When you have many millions of people with multiple, three dozen or more wastewater treatment plants dumping their pipes into the bay, then those nutrients build up," Rosenfield said. "What this whole thing is telling us is, the Bay Area, like many communities, its sewage treatment plants were built for a different time. And its sewage and stormwater capture systems were built in a different time – ’50s, ’40s – and that infrastructure needs repair."

Burke said it's an oversimplification to say the San Francisco Bay bloom was fueled by "poop and pee" as the Chronicle did – the sewage plants aren't pumping untreated human waste into the bay. But for the most part the nutrients do come from human waste – "poop water, how's that?" Burke said. The sewage plants, she said, aren't doing anything illegal.

"Their permits allow them to do what they do," she said. "What the rest of us are saying is those permits need to be reevaluated, and they need to be held to a higher standard."

Rosenfield and other scientists suspect that a generally warming climate, combined with increasing nutrient loads, could be part of the reason why algae blooms are becoming more common globally. But, he said, in the Bay Area, the temperature algae needs to form a bloom is exceeded under normal conditions, and "has been for decades." And while California's drought is affecting river flows, the impact that has on the San Francisco Bay is typically felt more in the winter and spring, he said. So, while climate change could be helping to set the table for more blooms generally – and it may have helped to trigger this summer's bloom in San Francisco – the massive bloom "could have happened without climate change, and it's been predicted for three decades," Rosenfield said.

Burke was blunt about what happened in the Bay Area this summer: "It's about nutrient load. And the nutrient load is coming directly from wastewater treatment plants."

The regional water board has told local agencies that it will likely require caps on nutrients in wastewater when their regional permit comes up in 2024, the Chornicle reported. While some local agencies have taken steps to reduce their nutrient loads, one now outdated study estimated it would cost $14 billion to upgrade the region's wastewater treatment plants, many of which were built in the 1970s and '80s. That price tag has likely increased. The Chronicle reported that fixing the plants could double or triple ratepayers' water bills, a heavy political lift.

"Angry constituents don't re-elect politicians in this area," Diener said. "And that's exactly what they'll have, because their water bills and infrastructure surcharges are going to skyrocket to fix this problem."

While many Bay Area cities have approved so-called "climate action plans," critics argue the region's leaders aren't doing enough to fund them or to protect the bay itself. Baykeeper, for example, is urging San Francisco Mayor London Breed to start investing in water recycling technology like many Southern California cities.

Last December, Breed unveiled a new climate action plan with lofty goals to electrify 150,000 city buildings and more than a million registered vehicles in the coming years, as well as convert almost all of the city's energy sources to renewables. But in her proposed budget this summer, Breed recommended against allocating any money to the city's Department of Environment to begin implementing the plan. The city's Board of Supervisors ended up approving only $2.6 million. San Francisco has the highest per-capita budget of any major city in the U.S., and had a record high $1.1 billion homelessness budget in fiscal 2021-22. It's also a city that apparently had enough money to spend nearly a half-million dollars in 2021 to develop new trash can prototypes because city leaders "weren't happy with the look" of off-the-shelf cans.

Rosenfield suggested that many of the fixes needed to lessen nutrient loads in the bay "are actually things we need to do anyway to solve other problems."

The sewage plants, for example, could be retrofitted to treat water at a higher level, while also protecting them from rising sea levels, he said. More investment in wastewater recycling could both improve water quality and help the region endure droughts. Likewise, restoring marshes and establishing more treatment wetlands could help soak up nutrients that contribute to algae blooms, while also protecting the coast from storm surge.

"There are many win, win, wins that come with solving this problem," Rosenfield said.