This article is part of The State of Science, a series featuring science stories from public radio stations across the United States. This story, by Joe Fitzgerald Rodriguez, was originally published by KQED.

Thousands of dead fish are piling up across the Bay Area.

From the concrete outer edges of Oakland’s Lake Merritt to the sandy beaches of San Francisco’s Fort Funston and the pebbled banks of Oyster Point in San Mateo County, the carcasses of fish likely poisoned by a harmful algal bloom — more commonly known as a red tide — are washing ashore.

It’s a mass-death event the San Francisco Bay hasn’t seen the likes of in years, says Jon Rosenfield, senior scientist with environmental group San Francisco Baykeeper.

“From a fish’s point of view, this is a wildfire in the water,” he said.

By SF Baykeeper’s count, the number of fish dying off in the San Francisco Bay could easily exceed hundreds of thousands, and that, Rosenfield said, might even be a “low” estimate.

His field investigator confirmed “easily tens of thousands of fish dead” in Lake Merritt alone. But Rosenfield cautioned, “What you see is just the hint of what’s actually happening further beneath the water’s surface and in places you’re not getting to on the shoreline. So it’s really an uncountable number.”

It may be harmful to humans, too. An algal bloom of this size can cause skin irritation and respiratory problems, and the San Francisco Bay Regional Water Quality Control Board is advising people to avoid swimming, kayaking or other activities on the water until the bloom subsides.

Mary Spicer of Alameda, who paddles on the bay with an outrigger canoe team, said some members of her team have been experiencing skin irritation after coming into contact with the water over the past few weeks. Spicer said she began to notice discoloration of the water about a month ago — and then it turned to a “denser, thicker, chocolaty brown.”

Paddling at the Oakland Estuary a couple weeks ago, she was heartbroken to see a juvenile harbor seal poking its head out of the discolored water. “Just to see these marine creatures … having to live in the red, brown, dense water, it’s really just disconcerting,” she said.

The National Oceanic and Atmospheric Administration describes red tides as a “harmful algal bloom,” or large colonies of algae plants growing out of control that are sometimes rust-colored. Not all algal blooms are harmful, and most are beneficial in the ocean.

However, a small percentage of algae can produce deadly blooms, and that’s what Rosenfield believes may be happening now.

SF Baykeeper is getting reports through its pollution hotline of dead fish in Foster City, Alameda, Keller Beach in Richmond, Sausalito and Fort Baker.

“Whatever number I offer you would likely be too low,” Rosenfield said.

Government officials KQED reached would not confirm any number yet. But on Monday, Eileen White, executive officer at the San Francisco Bay Regional Water Quality Control Board, described the algae bloom as “highly unusual” and “much more extensive” than blooms the agency has tracked in the past.

“And this one’s resulting in fish kills, which is not good,” she said. “So we’re going to continue to study, try to find the cause of it and learn from this, so hopefully we can prevent them in the future.”

Damon Tighe, who describes himself on his LinkedIn profile as an educator and a naturalist who studies mycology, tweeted a photo of a pile of dead fish at Lake Merritt on Sunday.

“Massive fish die off going on right now in Lake Merritt,” tweeted Tighe. “May be related to the HUGE algal bloom that’s been happening on the east bay since the start of the month in front of Alameda where effluent flows.” Tighe included a link to iNaturalist, a nature app that allows users to share their observations with other scientists and naturalists.

Massive fish die off going on right now in Lake Merritt #oakland #fish #lakemerritt

May be related to the HUGE algal bloom that’s been happening on the east bay since the start of the month in front of Alameda where effluent flows…https://t.co/1H1byxoWOk pic.twitter.com/FJBAU0InIb

— Damon Tighe (@damontighe) August 28, 2022

The algal bloom likely leading to the mass fish death is Heterosigma akashiwo, which SF Baykeeper and the San Francisco Estuary Institute and Aquatic Science Center have been tracking since it appeared in the last month. The aquatic science center noted that fish-kill reports began emerging around August 22, though they noted that the bay’s size makes data gathering a “huge challenge.”

What has changed, Rosenfield said, is those reports finally coming in, as well as confirmation from field investigators this weekend.

The algal bloom that Rosenfield says is most likely causing the die-off, he continued, is caused by a mix of environmental conditions, perhaps worsened by climate change, and treated sewage put out by wastewater treatment plants across the Bay Area. The red tide species of algae, Heterosigma, may be killing fish in two ways: It can produce a toxin that is deadly to fish, but it can also result in low dissolved oxygen levels in the water, which can also be deadly.

“So we’re not sure of which mechanism is operating here. Maybe it’s both,” Rosenfield said. But the same bloom has caused massive fish kills in other parts of the world, as well.

The change that spurred the bloom locally, Rosenfield said, was likely a tipping point in warming waters. The solution, then, is for wastewater treatment plants to begin recycling wastewater in far higher volumes than it does now.

An April 2022 report by the environmental group the Pacific Institute described wastewater recycling as underutilized across California. The group estimates that an additional 1.8 million to 2.1 million acre-feet per year of municipal wastewater is available for reuse in California.

San Francisco Supervisor Aaron Peskin, an avid swimmer with the South End Rowing Club, saw the red tide himself as he took a dip last week, on Tuesday, Wednesday and Thursday.

“My wife said I can’t swim in there anymore,” said Peskin. “I told her about it. It was like swimming through rust.”

He’s started to see the problem on the shores, too. His constituents have already started sending him photos of dead fish on San Francisco beaches. Peskin’s district includes Fisherman’s Wharf and the Embarcadero, areas with borders that touch the water. Peskin wants to ensure that those areas, and beyond, see climate action.

“Our public utilities commission, which is our sewer purveyor, needs to quickly come up with strategies to how San Francisco can do its part in reducing discharges that can exacerbate red tides,” Peskin said.

Reached over the weekend, Bill Johnson, chief of the wastewater and enforcement division at the San Francisco Bay Regional Water Quality Control Board, pushed back on the assertion that wastewater is to blame — the jury is still out, he says.

He says the water control board is spending $2.2 million annually to fund scientists studying the algal bloom to see if it is indeed caused by human wastewater.

“So if the solution is to ask the wastewater community to spend billions and billions of dollars for nutrients, then that’s what we’re going to do,” Johnson said. “But if the underlying causes are something else and if investing all that money isn’t going to solve the problem, we need to know that before we take that measure.”

Rosenfield countered Johnson’s statements by pointing to a 2020 report from James Cloern, senior scientist emeritus at the U.S. Geological Survey, that showed San Francisco Bay had “high nutrient loadings, primarily from municipal wastewater,” leading to the “potential for high algal production.”

Regardless, understanding what’s causing the algal bloom is crucial, Rosenfield said, because it is almost certainly not a one-off. Without preventive measures, this could be an annual occurrence, rising when the waters warm, and fading as they cool.

It’s already beginning to spook Rosenfield, who isn’t easy to spook — he’s been a senior scientist at SF Baykeeper for four years, and was a lead scientist at The Bay Institute for nearly 11 years. What really rocked him was seeing a number of a particular white sturgeon, a rare fish that’s part of a recreational fishery, show up dead on Stinson Beach. They don’t wind up dead nearly as easily, being large, armored fish.

“Seeing that sturgeon is an indicator of a much larger problem,” he said.

Like a canary in a coal mine, but with scales.

KQED’s Lesley McClurg contributed reporting to this story.