Nonprofits’ research projects on fish serve multiple purposes. They serve an impetus to improve restoration efforts and manage hatcheries better. They make a case for reintroducing species in areas where the species had a historical presence. And they draw funding, volunteers, allies, and media attention. When nonprofits undertake research projects on fish, their results can motivate entities with more funding, staff, and time to complete larger projects later. These parties may include colleges, universities, and government agencies.
In the South Bay, the region south of San Francisco in the Bay Area, a number of individuals and organizations are undertaking a number of research projects about fish. These projects are informing nonprofits and the public about the origins, populations, and health of local fish, including Chinook salmon.
Entities completing research projects on fish may receive donations, use their own funds, or apply for grant funding from the State through resource conservation districts (RCDs). RCDs are locally governed independent special districts that implement projects to improve soil and water.
Independent research projects provide information to chapters of national environmental nonprofits like the Sierra Club. The projects show such organizations that residents have an interest in their surroundings and are informed about environmental concerns. As the data come out, the environmental advocacy organizations gain avenues to approach local, state, and federal government entities about preservation. The advocacy organizations can use the projects to show why and how preservation should occur.
A) An image of a Chinook Salmon eye lens without the outer cortex taken on a Leica S9i with the accompanying software, LAS X. (B) A cross section image of a Chinook Salmon lens mounted in resin and taken on ImagePro scientific image analysis software. Image: Malte Willmes
SBCCC’s salmon project
In the July 2025 newsletter, CSPA shared an original story about the South Bay Clean Creeks Coalition (SBCCC)’s work to remove trash in the Guadalupe River Watershed, in and along Los Gatos Creek, the Guadalupe River, and Coyote Creek. The SBCCC is doing much more than frequent clean-ups. Members and volunteers are removing invasive plant species like anise and English Ivy from riverbanks. They are also revegetating, or replanting, spots along Los Gatos Creek with native species like local oaks.
SBCCC is currently collecting deceased Chinook salmon to study their health and origins. The group is allowed to do this because it has a Scientific Collection Permit from the California Department of Fish and Wildlife (CDFW). SBCCC began collecting fish in 2016 and has continued this effort into the present.
So far, the data indicate the fish are in adequate health. The fish sent in for analysis appear to be mostly straying fish from the Feather River and Mokelumne River fish hatcheries.
Dr. Malte Willmes, a Researcher for the Norwegian Institute for Nature Research (NINA) and the University of California, Santa Cruz, is the lead organizer of the effort to analyze the fish. He said the results regarding the fishes’ origin are not unexpected.
“These two hatcheries release a large number of Chinook salmon every year. These fish are known to stray into many different rivers when they return to the San Francisco Estuary and the Central Valley. We have found a few natural origin [wild] fish. We are now working on determining if these are coming from any of the Central Valley Rivers or if we are already seeing some local fish of Guadalupe River origin returning. It’s too early to tell,” said Willmes.
In the past five years, SBCCC estimates that every year, there are between 500 and 600 Chinook salmon in the Guadalupe River Watershed.
“Over the past 10 years, the number has increased every year. This is because of creek clean-ups by SBCCC and other organizations,” said Steve Holmes, Executive Director of SBCCC.
How SBCCC gets the job done
SBCCC members and volunteers usually collect Chinook salmon during the late fall. The group sends out a team of about 40 to 50 people.
“We come out when the fish are running. Some people are very good at spotting fish remains because they are members of chapters of Flycasters,” said Holmes.
SBCCC cannot collect living fish because its state permit restricts such activities. Chinook salmon are protected by state and federal law. In addition, the group wants to avoid collecting live fish before they spawn. The organization preserves remains by keeping them in a private freezer until sending them to a lab.
Between 2016 and 2024, SBCCC sent the remains to the Center for Watershed Sciences at the University of California, Davis (UC Davis). Since the organization started substantially increasing the number of fish it collected in 2022, it made plans to shift the analysis. In 2024, SBCCC started sending remains to the West Sacramento office of Cramer Fish Science (CFS), a Portland, Oregon-based fisheries research consulting firm that closely collaborates with UC Davis.
SBCCC has trained three to four members to do outreach and general education with the public. On some occasions, SBCCC has given out $50 gift cards to unhoused individuals living along the creeks who find and turn in fish.
“Between 2022 and 2025, we’ve given out $600 in gift cards. Some people found fish for us and did not take a gift card,” said Holmes.
Between 2016 and 2021, SBCCC sent in less than 10 fish per year, and 25 fish overall.
“From 2022, we have 26 fish, from 2023, about 70 fish, and from 2024, about 50 fish. For these fish we have otoliths, eye lenses, and material to perform genetic analyses,” said Willmes.
Below is a diagram that shows the methods that UC Davis and CFS have used to determine the origins of the salmon.
The order of lab processes to determine the origin of fish in the Guadalupe River Watershed. Image: Malte Willmes
The first screening tool is the presence of fin-clip and a micro-sized coded wire tag, which is implanted into the nasal cartilage of a juvenile salmonid.
“25% of hatchery fall-run Chinook in the Central Valley are tagged this way. This provides a wealth of information on the origin of those fish, like hatchery of origin, age, release sites, etc,” said Willmes.
The fish without tags are a mix of untagged hatchery fish and natural origin fish. The next step is to perform genetic analyses to check whether fish are coming from Coastal Chinook salmon populations or the Central Valley.
“So far all fish have come back as being from the Central Valley. For fish from the Central Valley, we then use eye lenses and otoliths to try and determine their hatchery or natural stream of origin,” said Willmes.
Scientists can use a fish’s eye lens, a part of the eye that sits behind the iris, to determine whether a fish fed on freshwater species early in its life. If a fish did so, this would indicate it is wild. If a fish fed on a marine-sourced diet, this would indicate it was raised in a hatchery. Hatcheries typically provide feed containing marine species to alevins (newly hatched salmon) and smolt (juvenile salmon).
Danhong Ally Li, Assistant Specialist at the Center for Watershed Sciences at UC Davis, peels Chinook salmon eye lenses. Image: Malte Willmes
Scientists can also examine a fish’s otoliths. These structures, also known as “earstones,” sit directly behind the brain. Otoliths can be used to reconstruct a fish’s age and growth. With geochemistry tools, scientists can identify where the fish spent their early years. SBCCC has collected water samples throughout the Guadalupe River watershed to provide a baseline map for these geochemical analyses.
George Whitman, Associate Specialist (left) and Kimberly Evans, Junior Specialist (right), both of the Center for Watershed Sciences at UC Davis, talk near a Laser Ablation Mass Spectrometer at UC Davis. This machine is used to analyze otoliths. Image: Malte Willmes
Willmes said the SBCCC has done an amazing job at collecting samples. Yet it could use more support. He would like to see other entities join in the SBCCC’s work to expand the study. These could include water, river, and watershed management agencies, cities, towns, and counties, and the public.
Holmes said raising awareness is key to forming partnerships.
“On several occasions in previous years, we approached the California Department of Fish and Wildlife (CDFW). We requested that they expand our Scientific Collection Permit to include the rescue of neighboring creeks to save trapped Chinook. They denied this request,” said Holmes.
Holmes added it is possible that CDFW would issue permits to organizations closer to those creeks.
How one man’s research hooks in
Dr. Rick Lanman is a Los Altos resident with an active medical degree who has served as the chief medical officer (CMO) for several biotech companies. He has had an interest in ecology for decades. In 2011, Lanman established the Institute for Historical Ecology, a Los Altos-based nonprofit. The purpose of this organization is to facilitate Lanman’s research on the past ranges of different species of native plant and animal species in California. Lanman has done several projects that focus on the San Francisco Bay Area. He funds most of the research himself, but has fundraised and received some financial support from anonymous donors.
In 2012, Lanman was appointed to the Board of Directors of the North Santa Clara County Resource Conservation District, formerly the Guadalupe-Coyote RCD. Lanman served for 10 years in that role, and is a past President of this Board. Lanman currently serves as an Associate Director of this Board. Lanman is in contact with the SBCCC and has volunteered with them as well.
Lanman’s first study focused on finding steelhead trout specimens to verify an old timer’s account. This project discovered museum specimens at the California Academy of Sciences which proved that during the 1890s, steelhead trout lived in the stream behind Lanman’s house in Los Altos. In 2020 and 2021, Lanman and several colleagues conducted ancient DNA analysis of the remains of Chinook salmon. The remains, which date between 1781 and 1834, were recovered in archaeological excavations on the historical Tamien Ohlone Rancheria of Mission Santa Clara.
“The DNA research showed that circa 1800, wild Chinook salmon were in the Guadalupe River. Later, these species were wiped out,” said Lanman.
In 2021, Lanman published the data from the Chinook salmon study in PLoS One, a peer-reviewed open access journal. The information attracted the attention of commercial fishermen, recreational fly fishermen, and Valley Water, Santa Clara County’s water district. In 2021, Lanman presented the data proving that Chinook salmon once spawned in the Guadalupe River to the National Marine Fisheries Service (NMFS). Lanman undertook this effort to request that San Francisco Bay be included in NMFS’s historical range map for California Coastal Chinook salmon. However, at the present time, the NMFS historical range maps for coastal salmon still omit San Francisco Bay tributaries.
Katja Irvin is the Conservation Vice Chair of the Loma Prieta Chapter of the Sierra Club, which covers the South Bay. She provided the following statement about Lanman’s work on Chinook salmon.
“The Sierra Club Loma Prieta Chapter has not been involved in advocating for recognition of Chinook salmon as native to the Guadalupe River watershed. However, through my involvement with the Loma Prieta Chapter Water Committee, I have followed Valley Water’s Fish and Aquatic Habitat Collaborative Effort since 2012. I have learned about the efforts to show that Chinook salmon have been historically present in the watershed.
The archeological study and analysis of middens at Santa Clara University, site of the Mission Santa Clara, including DNA analysis of fish bones, shows that steelhead trout as well as Chinook salmon were part of the diet of certain Native American groups in historic times. The nearest source for these fish would be the Guadalupe River. However, Valley Water is resisting any recognition that Chinook salmon are native and should be given the same protection as steelhead trout. Those have been recognized as native and listed as endangered. Valley Water raises doubt because Chinook do stray from their natal streams. So they could have originated elsewhere, like the hatchery strays that are found in the Guadalupe River today.
The Loma Prieta Chapter of the Sierra Club could advocate for Chinook to be recognized as native endangered species and for actions to be taken to specifically improve the habitat for Chinook salmon as well as steelhead trout. The Sierra Club generally supports habitat restoration to support native species. Adaptive management, such as stream flows that fit the Chinook lifecycle, is supported by our policies. However, to date we have just observed the efforts of more qualified parties such as the North Santa Clara Resource Conservation District, with leaders that include Rick Lanman and Roger Castillo; the South Bay Clean Creeks Coalition, led by Steve Holmes; and San Francisco Baykeeper (via a 2022 lawsuit regarding Valley Water’s actions and how they affect fish).”
Stephanie Moreno is the Executive Director of the North Santa Clara Resource Conservation District. She said that in 2020, the RCD’s Board of Directors decided to withdraw from the Fish and Aquatic Habitat Collaborative Effort (FAHCE) Settlement Agreement. The shift was due to extended delays in implementing the agreement and expected revenue impacts from the COVID-19 pandemic. This decision was proceeded by a shift in RCD priorities.
“In 2014, the Board of Directors decided to direct more focus to providing services to agricultural producers and to addressing climate resilience in urban neighborhoods. We continue to support the work of other entities to restore and protect fish and habitats for them by offering grants and “pass-through” federal and State funding for projects that improve local watersheds,” said Moreno.
The North Santa Clara RCD is using State funding to help implement the Los Gatos Creek Watershed Restoration Project. The current budget for the project is $392,076. The money will support restoration of streams and tributaries of the Los Gatos Creek Watershed. The South Bay Clean Creeks Coalition (SBCCC) is a partner in this project.
One component of the project is gravel augmentation in Los Gatos Creek. This will improve spawning habitats for steelhead trout and Chinook salmon.
“The money goes to reimburse subcontracting entities for their costs installing the projects, including gravel, supplies, planning, and dollars spent on community outreach and education. The grant runs for five years,” said Moreno.
Moreno said Lanman’s article on Chinook salmon generated a lot of discussion when it first came out.
“But now it’s been a few years. His historical archaeological research laid the foundation for protection. The current work, the restoration, is helping the fish,” said Moreno.
Irvin and Moreno’s statements show that fish research projects are a good start. Yet it takes environmental activists, educators, and nonprofits like CSPA to utilize that data to fight harmful projects, from reservoirs to dams, large water diversions, and pollution.
Building a path from the data to the City Council meeting, the classroom, and the Administrative Hearings Office of the State Water Board is critical. The more independent research projects that are done, and the more organizations that do them, the more potential there is for targeted partnerships to effect substantial change.