Scientists are hard at work trying to home in on the cause—or likely causes—of the algae bloom that's led to mass death for marine life. Credit: Amir Aziz

“Mystery epidemic kills fish in Lake Merritt,” announced an Oakland Tribune headline. 

“The lake water became a rusty color,” another journalist reported, causing “the drowning of countless bass.” 

Sound familiar? Those reports come from newspapers in 1939, when a mass fish die-off, not unlike this week’s tragedy, struck the lake.

Over the course of history, the waters of Lake Merritt and the bay it’s attached to have lost marine life to both natural and human forces. In 1939, scientists attributed that year’s mass death to an invasion of microscopic aquatic creatures.

This time, the cause of death is a massive bloom of the algae species Heterosigma akashiwo, which appears to be depleting all the oxygen in the water and possibly emitting toxins. 

But what is causing the algae bloom?

That’s the “billion dollar question,” said Eileen White, executive officer of the San Francisco Bay Regional Water Quality Control Board, which monitors water conditions. 

Nobody knows the answer yet, and there’s likely to be more than one cause, but researchers and citizen scientists are rushing to learn as much as they can before the evidence—dead fish and rusty water—rots or floats away. 

Read on for the most credible theories so far and more fascinating history of fish kills in Lake Merritt and the bay over the past 100 years.

First, a little more about why fish are dying

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Dead fish line the Lake Merritt shore after an algae bloom disrupts oxygen levels in the water. Credit: Amir Aziz

The algae bloom was initially spotted off Alameda island in July before spreading rapidly to the Oakland Estuary, Lake Merritt, and other parts of the San Francisco Bay. Discoloration of the lake, which turned a deep rusted red, was an early sign something was wrong.

Starting last weekend tens of thousands of dead fish—anchovies, striped bass, smelt, and even large bat rays—washed ashore, piling up around the lake and causing horror among people who visit and study it.

There are a couple of possible reasons the algae bloom killed so many fish. Abundant algae can consume large amounts of oxygen, especially when they die and decompose, leaving little for other marine life that depend on it. Tests have confirmed extremely low levels of oxygen in the water over the past week.

The algae may also be producing a toxin that kills the fish, and their decomposing bodies may be what’s using up the oxygen, said Quay Dortch, a senior scientist with the National Oceanic and Atmospheric Administration who studies harmful algal blooms.

“Heterosigma is known for being toxic, but nobody’s ever figured out how it’s toxic”—you can’t detect the toxin through tests, Dortch said.

Either way, once the oxygen is depleted, it won’t easily replenish in a relatively stagnant body of water like Lake Merritt.

“There’s just that small channel” connecting to the bay, limiting water-mixing, said Keith Bouma-Gregson, a biologist with the USGS’s California Water Science Center. “It’s harder for new oxygen to get in the water as a result of that.”

Toxic or not, why has the algae proliferated around the bay? 

A prime suspect: wastewater nutrients flowing into the bay

Heterosigma akashiwo and other organisms that cause “red tides” require nutrients like nitrogen and phosphate to grow. They’re naturally occurring compounds, but a big source is human activity.

Nearly three dozen sewage plants discharge between 300 and 500 million gallons of treated wastewater into the bay each month, according to Bay Area Clean Water Agencies, a regional government agency that coordinates all the sewer districts in the bay​​. This wastewater contains the exact types of nutrients that algae feed on. 

The algae bloom started in Alameda and quickly spread to other parts of the bay. Here, a dead sturgeon turns up at Richmond’s Point Isabel. Credit: Darwin BondGraham

“Wastewater treatment facilities represent two-thirds of the nutrient loads to the bay,” White said. “Every day when you flush that toilet, you’re sending nutrients to your local wastewater plant, and they don’t treat for that.”

So did wastewater outflows into the bay recently spike? Or have nutrient levels been rising in wastewater in recent years? The most recent report from Bay Area Clean Water Agencies (BACWA) shows that altogether the Bay Area’s sewage districts haven’t increased the amount of wastewater they’re dumping in the bay over the past 10 years. And the nutrient loads in this water haven’t notably increased. 

Lorien Fono, executive director of BACWA, said nutrient loads to the Bay are at similar or lower levels than in previous years. “Our understanding is that a bloom of this size can’t happen without access to nutrients, but we don’t understand what triggered this event,” she said. 

Some facilities elsewhere remove nutrients from waste before it’s discharged into the ocean or rivers. This can go a long way in preventing blooms of algae and phytoplankton. The Water Board could require the region’s wastewater plants to treat for nitrogen and phosphorus, but it would be an expensive endeavor. 

In fact, a major Sacramento wastewater plant was recently upgraded to reduce its nutrient outflows, which feed into the bay. “Between the Sacramento upgrade and the decrease in loading from the Bay Area wastewater agencies, the aggregate loading of nitrogen to the Bay is the lowest that it has been in at least a decade,” said Fono.

White said the Water Board is currently studying the impact of nutrients in the bay to determine whether regulating local plants would be appropriate.

“Everyone in the Bay Area will have to pay for that on their wastewater bills,” she said, “so we want to make sure it’s based on sound science.”

Dortch said removing nutrients is always a good idea but cautioned against going too far. “You need some algae in the water because that’s what feeds fish, so you don’t want to remove everything,” she explained.

Is agricultural runoff the culprit?

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A sting ray sits belly up in Lake Merritt where many fish are dying from the algae bloom impacting the water. Credit: Amir Aziz

Another source of nutrients is water draining from the Central Valley’s vast fields of fruits, vegetables, and grain farms. Fertilizers that farmers apply to their crops help plants grow, but lots of the nitrogen and phosphorus and other compounds drain into creeks and rivers that feed into the Delta. The Delta then sends this nutrient-rich freshwater into the San Francisco Bay.

But like wastewater from urban sewers, it’s not clear that there was any big increase in runoff from farms this past year or that farmers used more fertilizers than in past years. So why would the algae bloom be so explosive this year?

One theory we’ve been asked about is whether cannabis farming could be adding nutrients to the bay. Cannabis grow warehouses have proliferated in Oakland, Richmond, and many other Bay Area cities in recent years. Some speculate that unpermitted grow operations could be dumping their wastewater—comprised of strong fertilizer solutions—into storm drains that empty into the bay. 

But so far, no one has shown any evidence this is happening, let alone at the scale that would be needed to cause a massive algae bloom.

Are climate change and the drought playing a role?

This winter, California weathered the driest January through March on record in over 100 years. Rain levels were abysmal, and runoff from rivers into the bay was minimal as a result. 

That runoff is needed to flush out the water, avoiding the stagnant conditions that algae can thrive in. The runoff also dilutes the bay and reduces salinity, or salt levels. Some experts have speculated that without that dilution, the brackish water in Lake Merritt and the rest of the bay may be saltier than usual, creating an environment allowing heterosigma, which needs some salination, to grow.

“The seawater is not diluted out, so you might hit that salinity range that heterosigma likes to grow in if you’ve had a period of very low flow,” Dortch said.

Scientists have also looked into whether rising temperatures caused by climate change could be warming the water, creating another algae-prone environment. 

However, Bouma-Gregson said that both water temperatures and salinities appear to be at standard levels in the bay this summer.

“Heterosigma usually bloom in warmer waters,” starting around 59 degrees, he said, and his team—which has been taking research boats out on the bay since the first appearance of the algae in early August—have tracked temperatures of about 68 degrees, which is “not that unusual” for this time of year. 

It’s surely a combination of factors

It may not be any single factor causing the crisis. Dortch said that the nutrient levels likely interacted with the climate conditions to spur the algae bloom. 

“If it’s a low-flow year, and you have the right salinity, and you have the right temperature, and you have the right nutrients, then you’re going to have a bloom of some kind, and the exact conditions will determine what kind,” she said.

Dortch noted that harmful algal blooms happen on their own in nature but speculated that “anything as extreme as what you’re seeing is probably not naturally occurring.” 

But almost all the potentially dangerous factors that could have played a role in the current bloom are necessary in moderation.

“All the things we love in the ocean depend on phytoplankton being able to grow and photosynthesize,” said Bouma-Gregson. “It’s when we see too much of it that we see harmful effects.”   

We’ve been here before. Here’s what people think caused fish kills over the past 100 years

Lots of media reports about this past week’s marine life die-off have called the event “unprecedented,” but as local geologist Andrew Alden (see our Q&A with him on Oakland’s natural history) noted recently, there have been lots of fish kills in Lake Merritt’s history.

In June 1939, a “mystery epidemic” killed fish by the thousands in Lake Merritt, causing bass and anchovies to wash ashore in piles. Researchers immediately homed in on a tiny kind of animal plankton called a rotifer as the cause. Multiplying by the billions, the rotifers consumed all of the oxygen in the water, according to the state Fish and Game Commission. The city hauled dead fish away in trucks and “flushed” the lake by opening the tidal gates.

A decade later, “well over 100 bass, most of them weighing over 15 pounds” died and washed up on the Lakeshore Avenue side, according to the Oakland Tribune. State and local authorities blamed sewage flows from homes and businesses directly into the lake for polluting the water and killing the fish. The sewage might have caused an algae bloom that sucked oxygen from the water, or killed the fish with toxins.

Fish kills became less common in Lake Merritt after the 1950s, after all the city’s sewage started to be piped to the East Bay Municipal Utility District’s plant and treated before being released into the bay.

But plankton and algae blooms continue to be a force of nature in the bay and across California’s shoreline, and they’ve likely been amplified by human activity.

Cleanup crews load dead fish into a wheelbarrow at Lake Merritt in 1939. Credit: Oakland Tribune/

In 1961, there were numerous reports of fish die-offs in the Bay Area, including Petaluma Creek, Carquinez Straits, and Guadalupe Slough in the South Bay. Among the dead were sturgeon, shad, anchovies, and catfish.

The year 1964 saw one of the biggest red tides and fish kills in state history. Ten million fish perished in Southern California, reported the Los Angeles Times. The biggest fish kills happened near where three wastewater pipes emptied into the Port of Los Angeles and another location where oil well wastewater was dumped into Marina Del Ray. Santa Cruz’s harbor was carpeted with dead sardines and the deadly effects were felt at least as far north as Fort Bragg, where dead herring washed up in Noyo Harbor. State researchers blamed Gonyaulax polyhedra, a dinoflagellate that used up all the oxygen in the water and produced a toxin.

Ten years later another red tide bloomed off California’s central coast. Fishing boat captains complained of pulling up pots filled with dead crabs, and fish washing ashore around San Luis Obispo and Huntington Beach in Orange County, where the city scooped a quarter million carcasses up and turned them into fertilizer for city parks.

San Luis Obispo was affected again in 1997 when a red tide drifted through giant cages in the bay holding salmon that were being raised as part of a state fish stocking program. Around 28,000 fish died from lack of oxygen and toxins.

Since then, scientists have documented numerous harmful algae blooms and red tides along California’s coast, involving dozens of kinds of microorganisms, some that produce toxins that kill fish and can harm and kill humans, and others that use up all the available oxygen in the water—or both!

Who is going to figure all this out?

Oakland workers remove hundreds of pounds of dead fish from the lake. Credit: Ricky Rodas

A number of agencies and nonprofits are working on long-term studies of the San Francisco Bay, including the Water Board, the San Francisco Estuary Institute, BayKeeper, the USGS, the U.S. Environmental Protection Agency, UC Santa Cruz, and UC Davis. 

The Bay Area Clean Water Agencies and the dozens of sewer districts it coordinates are helping to fund research through the Nutrient Management Strategy and Nutrient Science Program, housed at San Francisco Estuary Institute.

Questions on scientists’ minds include why the bloom started in Alameda and the Oakland Estuary, why it spread where it did, and what eventually stopped it, said Bouma-Gregson.

And one of the most powerful contributions to our collective understanding of the bay is being made by unofficial scientists and local institutions, like the Lake Merritt Institute and Rotary Nature Center Friends, who are always keeping an eye on conditions at the lake and spreading the word. For more on life in the lake, and the community members who study it, see our illuminating piece from 2020.

Natalie Orenstein covers housing and homelessness for The Oaklandside. She was previously on staff at Berkeleyside, where her extensive reporting on the legacy of school desegregation received recognition from the Society of Professional Journalists NorCal and the Education Writers Association. Natalie’s reporting has also appeared in The J Weekly, The San Francisco Chronicle and elsewhere, and she’s written about public policy for a number of research institutes and think tanks. Natalie lives in Oakland, grew up in Berkeley, and has only left her beloved East Bay once, to attend Pomona College.

Before joining The Oaklandside as News Editor, Darwin BondGraham was a freelance investigative reporter covering police and prosecutorial misconduct. He has reported on gun violence for The Guardian and was a staff writer for the East Bay Express. He holds a doctorate in sociology from UC Santa Barbara and was the co-recipient of the George Polk Award for local reporting in 2017. He is also the co-author of The Riders Come Out at Night, a book examining the Oakland Police Department's history of corruption and reform.