In 2022, the HAB-pocalypse happened. All across the San Francisco Bay, harmful algal blooms popped up. Toxins from the bloom killed hundreds of fish, including endangered sturgeon, and prevented hundreds of swimmers and fishers from enjoying their favorite spots.
Harmful algal blooms, or HABs, turn waters anything from brown to green when phytoplankton, microscopic organisms that love to hang around the tops of sunlit water, go into overdrive. Warm and sunny summers mix with slow moving waters and excess nitrogen, causing the phytoplankton colonies to grow out of control. Blooms can produce toxins, eat up oxygen, clog up waterways, and make waters unsafe for swimming.
The Bay’s reputation for having excessively nutrient rich water is partially thanks to wastewater treatment plants overflowing, dumping raw sewage into waterways. Bad blooms are hard to predict, but one thing’s for certain: nutrient pollution from raw sewage and agricultural runoff doesn’t help.
But until the summer of 2022, the Bay had existed mostly bloom-free. Then heterosigma akashiwo, also known as the ‘flying potato’ by researchers, caused the first-ever Bay-wide harmful algal bloom. And nobody really saw it coming. Because nobody was keeping tabs on these problematic phytoplanktons in the Bay Area. Before the heterosigma event, the San Francisco Estuary had no sustained monitoring programs for saltwater harmful algal blooms.
Motivated by this gaping hole in monitoring, San Francisco Baykeeper, a nonprofit organization aimed at holding polluters accountable, began to sample water across the Bay for bloom culprits. The program—whose official name is Monitoring and Event Response for Harmful Algal Blooms—launched in the summer of 2024, with help from the National Oceanic and Atmospheric Administration, US Geological Survey, and the SF Estuary Institute.
Cheryl Patel, Baykeeper’s field investigator and community science coordinator, trains community members to become community scientists. “Anyone can be a volunteer,” says Patel. “It just requires a good time commitment in the summertime.”
In a summer camp-like fashion, volunteers begin the sampling season at an all-day workshop led by the program coordinator from NOAA’s Phytoplankton Monitoring Network. There they learn to ID phytoplankton species and make a microscope do their bidding.
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Data collected by the volunteers accomplishes a couple of goals. It is added to NOAA’s Phytoplankton Monitoring Network, aiding a nationwide effort to study these organisms’ behavior and changes year to year. But locally, Baykeeper hopes to funnel all that water sampling data into a dashboard where resource managers—and the public—can check the Bay water quality near them.
“They’re excited about being supportive and helpful in a tangible way with our Bay’s health,” says Patel.
A day out at the lagoon
Today, a handful of volunteers are out sampling at the Alameda Seaplane Lagoon, which sits on the south side of Alameda Island. A known problem child ,the lagoon is kept under the watchful eye of the Baykeeper community science monitoring program each summer.
“This is actually the site that kind of started it all, in a way, because in the 2022 bloom, things started showing up here first here in Alameda,” Patel recalls. “We would get phone calls from the public saying, ‘Hey, we’re seeing discolored water?’ For some reason, in 2022, it really exploded.”
The lagoon is just one of nine sampling sites spread across San Francisco, Richmond, Berkeley, Alameda, and San Mateo shorelines. But now in their third year of monitoring and 14 volunteers strong, Baykeeper is working to establish new sites in the South Bay.
Monitoring at the lagoon starts as soon as the time is checked and jotted down—11:42 a.m. Next, a look at the tide charts. A high tide is coming in, with water barely hitting the feet of some of the volunteers on the ramp. Patel holds a clipboard with a long list of things to check—tidal height, air temperature, water temperature, and salinity.
Snooping over the edge of the concrete lagoon ramp, Diane Livia, a recurring volunteer, pulls out a small rod-like contraption from the box of scattered supplies. She turns to her first-timer grandson, Kiern Holbrook, to explain how the refractometer works, “You have to try to keep this level and point it towards the sun, so you get the most light. The light refracts off this prism, and then it tells you how many particles of salt are in the water. That’s how we get our salinity measure.”
Holbrook peers through and exclaims, “Kind of feels like using a binocular!”
The last piece of data we need is Secchi depth, a way to measure the turbidity of water. Livia takes a piece of string attached to a disk split into black and white and starts slowly dropping it into the water. The goal is to stop the string when the disk is no longer visible. Then Livia and Holbrook pull it back up, measuring the length of the wet portion of the string.
Now, we’re ready to collect our phytoplankton water sample. Aptly named, Livia grabs ahold of the plankton net and submerges it in the water. “Now we have to walk it,” she explains. “It’s like walking a dog that doesn’t know where to go.”
Livia and Holbrook spend the next three minutes delicately dragging the net across the water until Patel’s timer goes off. They carefully place the water sample into a squeeze bottle and bring it over to Patel.
“This is the bottle we’re gonna bring to the microscope and take samples out of,” says Patel.
Under the scope
Phytoplanktons in water, all jarred up, we walk from the lagoon ramp to a shaded area with tables and benches. There, Patel sets up a microscope connected to a small power generator, which the volunteers will peer through in search of 12 kinds of phytoplankton species. “Are they there or not?” says Patel. “They could be harmful if they bloom — reproduce and make billions.”
Patel pours a few drops of the water sample into a microscope plate and begins to adjust the knobs.
It’s Holbrook’s turn and his first time ever looking under a microscope. He starts peering around and says, “I can’t identify floating things. I don’t know if they’re like critters or just like floating things.”
Patel takes back the reins and moves the sample around until she spots something. “The hard part is there’s a lot of lookalikes,” she explains. “So with this one, you can tell that it’s Chaetoceros because if you look at each little square, you can see that there’s four little spines.“
Chaetoceros is a marine diatom that makes chains, and each link in the chain has four spines. Some species in this genus are known for forming algal blooms, making it one of the target species for today.
Patel moves on from this diatom and spots a dinoflagellate. “This is the Akashiwo sanguinea, and it’s smooth. It’s swimming around,” she says. “This one’s nickname is the golden tooth because it kind of looks like it has tooth roots as its little hypotheca.” Holbrook peeks in and pipes up, “Oh, I like it! It swims.”
Normally, volunteers like Livia use cheatsheets full of pictures of the 12 target species, and NOAA even has a “Phyto” App to help with identification.
“There’s a lot. It’s alive,” says Livia. “It was quite illuminating to me—the number of things that were moving on their own. All these different shapes, right?”
If volunteers happen to spot a target species, they wait until its numbers pass a certain threshold, then they alert the HABs coordination team, made up of a bunch of organizations around the Bay. They also ship a sample of the problem phytoplankton mixed with some preservatives to the California Department of Public Health and other partners throughout the country.
After the phytoplankton party
When the algal monitoring season is over, the work isn’t done. Baykeeper uses the data collected by volunteers for advocacy work, “That’s why it’s so important to collect this data because Baykeeper advocates,” says Livia. “We go to the water board. We go to the state. We’re always trying to tighten up the regulations, and that issue of treating the sewage more fully is strictly political.”
Nutrient pollution is one of the major factors contributing to blooms, and waste water treatment is a big portion of that pollution.
“There are many factors to an algal bloom, but the sewage is the main one because that’s the nutrients that these algae are going to live on, and that’s what allows them to multiply and multiply and multiply,” says Livia.
San Francisco is one of a few cities that has a combined sewer system, meaning stormwater and wastewater both go into the same set of pipes and get treated together.
But after big rains, wastewater treatment plants are likely to be overwhelmed and begin overflowing with raw sewage. This sewage usually makes its way into Bay Area waterways, making it one of the most nutrient-rich bodies of water in the world. That’s how the phytoplankton get fed.
For the past few years, Baykeeper has collaborated with regional groups to require wastewater treatment plants to reduce their nitrogen load into the Bay. In 2024, Baykeeper filed a lawsuit against San Francisco over the 1.2 billion gallons of raw sewage and runoff making its way into the Bay.
“Blooms will happen, but it’s the matter of a bloom being allowed to continue for so long and get so big and expand the way it did,” says Patel. “And part of that really is the excess nutrients put into the Bay from wastewater treatment effluents, and we wouldn’t have been able to make that connection without the data.”
As long as there’s water to sample, people will continue sampling. “I think it’s heartening to have people always asking, ‘Hey, do you need volunteers? We looked at plankton at this site, maybe we can add to the public dataset.,’” says Patel. “I think that’s my favorite thing about community science is that people come out of the woodwork as soon as they see, ‘Oh, there’s there’s a space for me to fit in here, or there’s opportunity to learn.’”
