Did Salmon Always Live in San José?

June 24, 2020

After an absence of many decades, Chinook salmon swim up the Guadalupe River in San José most winters. The fish look for places to lay eggs and often find them. If there’s enough water left in the dry season, their offspring swim back down the river in the spring to head out to sea.

Surprisingly, given the generally heated politics regarding fish in California, little else is known about these salmon. Almost no one will dispute that for some matter of decades until the 1980s, salmon did not swim in the Guadalupe. So where do these modern fish come from? Why do they choose the Guadalupe? Are the fish that swim up the Guadalupe returning to it after having hatched there, or are they strays from elsewhere that find it anew every year? How many salmon chose the river before Europeans and Americans arrived and altered the environment beyond recognition, and should that matter one way or the other in what we do about the fish that swim in it now?

The Guadalupe-Coyote Resources Conservation District, which for decades has fought the Santa Clara Valley Water District over water flows and habitat protections for salmon, reported in March that it had found a new way to demonstrate the historic presence of the fish in the watershed. If they can demonstrate that the fish were native to the stream, the RCD says, it follows that salmon merit greater protections than Valley Water has so far granted them.

To support its claim, the RCD looked at fish bones found in the area of the Santa Clara Mission where Indigenous “neophytes” lived. More than 17,200 fish bones were recovered from a 2012-2013 archaeological excavation led by Santa Clara University Cultural Resources Management Director Linda Hylkema and Albion Environmental senior archaeologist Cristie Boone. Of those bones, 55 came from some species of salmonid, meaning either salmon or trout. The RCD sent those 55 bones to Brian Kemp, a professor at the University of Oklahoma who specializes in ancient DNA, to untangle what was what. In a presentation intended for an annual Salmonid Recovery Conference in Santa Cruz in April 2020, Lanman reported that three of the 55 bones had come back as belonging to Chinook salmon.

“This study provides the first physical evidence that Chinook salmon were historically native to the Guadalupe River watershed, the southernmost major metropolitan area hosting salmon runs in the United States,” Lanman wrote in an abstract of his presentation, which was never delivered after the conference was canceled due to COVID-19.

In a phone call in early April, Lanman said he wants the study to help convince people to support the salmon. “Chinook salmon have not been part of the plan. I want citizens to understand they should be,” he said. “San José is the southernmost city with a salmon run, right through downtown! All we have to do is help it out a little and it should rebound.”

In a statement, Valley Water spokesperson Mark Gomez responded that the district’s biologists think it’s likely there are more salmon in the Guadalupe now than there were ever in the river historically. There’s no observational record of Chinook salmon in Santa Clara County before 40 years ago, Gomez wrote. And California’s boom and bust precipitation wouldn’t have made this hospitable ground for salmon. “Historical flow conditions associated with the Mediterranean climate did not provide consistent access to the upper watershed and its spawning habitat,” Gomez wrote, “making potential occurrence opportunistic and rare.”

The district is already making river and stream improvements for federally listed steelhead trout, Gomez added. Any salmon that do find the river should benefit from those improvements.

Brian Spence, a fisheries biologist at NOAA’s Southwest Fisheries Science Center in Santa Cruz who has studied the historical range of salmon, also called the fish opportunistic. Though salmon are justifiably famous for their ability to wander thousands of miles around the ocean and then find their way back to a spot within a few feet of where they were born, some percentage elect to forge a new path. It’s not just a “failure to home,” scientists say, but a useful compliment to homing. “Straying can be adaptive over short ecological time frames and at longer evolutionary scales,” fisheries scientists Matthew Keefer and Christopher Caudill wrote in a 2014 article in the journal Reviews in Fish Biology and Fisheries.

Still, this independent streak in salmon populations makes it very difficult to tell where salmon were and were not in California. The fish range widely, Spence wrote in an email, “continually testing the limits of their distribution.” Early European and American observers weren’t reliable recorders, either, often mistaking the various salmonid species for each other. Taxonomic reshuffling since the 1800s has further complicated the picture of what any of them even reported seeing. And by the time those observers were wandering California in the middle to late 1800s, settlers had already transformed the waterways.

“Use of certain rivers and streams in the Bay Area by salmon was probably episodic, with fish occupying those streams during wet years with good early winter stream flows, but absent during periods of drought,” Spence wrote. “Historically, with hundreds of thousands (if not millions) of fish returning to the Sacramento-San Joaquin Basin each year, it is reasonable to suspect that Chinook salmon at least periodically used the Guadalupe and other Bay Area rivers when conditions permitted.”

Based on DNA taken from salmon in the Guadalupe in the late 1990s, the river was recolonized by hatchery fish from several places, including the Central Valley and Russian River, and even some strays that appeared to come from as far as the Klamath and Columbia Rivers. But whatever the origin of those first fish, Lanman says that now he and his RCD colleagues increasingly find fish without tags or clipped adipose fins, the telltale marks of a hatchery upbringing. To him this means that perhaps salmon have once again made the Guadalupe River home. “Maybe,” Lanman says, “our fish are self-sustaining.”

In mid-June, the RCD announced it was withdrawing from the Fish and Aquatic Habitat Collaborative Effort, a 17-year-old settlement agreement with Valley Water and numerous other government agencies and NGOs. The FAHCE was meant to resolve disagreements about water flows and salmon habitat in the Guadalupe River, but the effort has been stalled for years. “As much as we regret needing to leave the FAHCE agreement at this time, it is important for our District to redirect and focus its limited resources on projects and programs with more certain timelines and outcomes,” Lanman wrote in a press statement announcing the decision.

In a reply, Valley Water CEO Norma Camacho wrote in a statement that the district would continue to prioritize fish habitat restoration and enhancement. “While Valley Water’s Board of Directors evaluates the next steps,” Camacho wrote, “this does not change our commitment to stream stewardship and improving fish habitat in Santa Clara County as part of our flood protection and water management activities.”

About the Author

Eric Simons is a former digital editor at Bay Nature. He is author of The Secret Lives of Sports Fans and Darwin Slept Here, and is coauthor, with Tessa Hill, of At Every Depth: Our Growing Knowledge of the Changing Oceans.