Scarce flows, hungry predators, warm water, and politics conspire against salmon in the Delta, but which is the dominant stressor? Reporter Alastair Bland interrogates the science.
By Alastair Bland
As California’s Chinook salmon fishing season sits on pause for the third consecutive year, the future of the species dangles in the balance. The fish, historically abundant, now hover near record lows, with the adult population in coastal waters and Central Valley rivers representing about one tenth of late 20th century averages.
The precipitous crash has stakeholders on edge, and how to turn it around is an urgent matter of discussion among scientists, officials and the fishing community. Many experts say that reviving the state’s Chinook salmon runs is, in principle, a simple task: Restore the river and riparian habitat vital for migration and spawning, and the fish will return.
But there is another element in the mix: nonnative predators. Fishes including largemouth bass and striped bass, introduced to California decades ago, eat many young salmon born in the Central Valley. It’s a problem that some farmers, lawmakers and scientists want to tackle with targeted predator removal programs. This approach, they have argued, could be the best unused tool in the salmon recovery toolbox.
“We’ve been trying the same things, regulating flows and habitat restoration … for 20 or 30 years, and here we are in the third season of a salmon fishery closure,” said biologist Dana Lee, who works for the private research firm FishBio and has been studying nonnative predator impacts on salmon in the Stanislaus River, a San Joaquin tributary. “These things don’t seem to be working, so what other options do we have?”
Lee believes the state should relax or remove fishing restrictions for nonnative predator species – what he calls “the easiest no-brainer” amendment to the rules and policies affecting the salmon’s freshwater environment.
But is the predator problem an elephant in the room or just a red herring? While all experts agree that being eaten is a common fate for small salmon, few scientists name predators – even invasive ones – as a primary factor in the collapse of California’s salmon. Jon Rosenfield, science director at San Francisco Baykeeper, said that to observe that most young salmon die in the mouths of predators fails to explain why they do.
“What made the predator successful and the smaller fish unsuccessful is the question,” said Rosenfield, a veteran in the fight to save the San Francisco Estuary’s ecosystem.
Biologist Andrew Rypel, formerly a professor at the UC Davis Center for Watershed Sciences, fears that targeting predators – even invasive ones – misses the mark.
“The danger is we’re shifting the blame over to predators when the real problem is that the habitat has deteriorated,” he said. “I worry that we’re taking our eye off the ball.”
It’s Something in the Water
The most immediate problem dogging Central Valley Chinook is simple: A few weeks or months after the adult fish spawn and naturally die in freshwater, most of their offspring perish. This often happens in the egg stage, when lethally warm outflow from dams can kill large numbers of fertilized eggs.
Once juvenile Chinook have developed into fry, parr and smolts and begun their downstream migrations, predators – including birds and otters but also nonnative fishes – become a leading cause of death. Some years, virtually no juvenile salmon born in the Central Valley’s rivers successfully migrate to the ocean.
But there is a difference, several sources explained, between the immediate cause of death – often, being eaten – and the ultimate cause. To identify the latter, most scientists are looking upstream, and what they’ve found, in one scientific study after another, is that reduced river flows between late-fall and spring correspond to lower survival of juvenile salmon migrating to the ocean. Conversely, more water tends to mean higher survival, the research shows.
Such findings suggest that chronically low river flows – the impact of drought and heavy diversions to farms that increased for decades – are the ultimate cause of high juvenile salmon mortality and probably a key factor in both habitat degradation and the dire status of California’s salmon populations.
In the wet year of 2019, an estimated 979,000 juvenile Chinook survived a 34-mile stretch of downstream migration on the Stanislaus River, with a start-to-finish survival rate of 59%, according to data published by FishBio in the journal San Francisco Estuary and Watershed Science in 2023. But in the critically dry 2021, only 30,264 fish completed this segment of their migration, with a survival rate of 26%.
Similar data comes from the Sacramento River, where extreme drought conditions in 2020-2022 led to disastrously poor Chinook survival. Between 0% and 5% of tagged fish in different release groups, tracked as they migrated to San Francisco Bay, survived those years, while California’s blockbuster wet year of 2023 saw survival rates as high as 50%.
“The research is pretty clear that more water is better for fish,” said UC Santa Cruz biologist Cyril Michel, who has studied salmon in Central Valley rivers since 2007. In at least 10 published studies, Michel and his colleagues have found a strong connection between flow and juvenile survival, with some of their work additionally demonstrating that wet years correspond to increased returns of adult salmon two to three years later.
Other scientists have independently found similar results. Researchers Dalton Hance and Russell Perry, of the USGS Western Fisheries Research Center, coauthored findings in the Canadian Journal of Fisheries and Aquatic Sciences in 2021 showing that survival of emigrating Chinook smolts in the lower Sacramento River decreased rapidly when river flows dropped below about 35,000 cubic feet per second. In a related paper in 2022, they reported that salmon “survival decreased with decreasing river flows and increased water temperatures.”
“What we’ve clearly seen from literally dozens of very recent papers … is that [salmon] die more when river flows are low than when river flows are high,” Rosenfield said.
Ample flows have a variety of direct and indirect benefits for salmon. They help flush juveniles safely downstream to the ocean. Higher flows tend to keep the water suitably cold – vital for salmonids. Higher river levels also allow small fish to access riparian habitat features, like floodplains and side channels
Low flows, on the other hand, mean a slower journey downriver, often in clear, warm water conducive to the metabolism and visual hunting tactics of black bass. Rosenfield noted that reduced flow levels concentrate fish populations in a smaller body of water, increasing each prey fish’s odds of encountering a predator fish.
Carson Jeffres, a senior researcher at the UC Davis Center for Watershed Sciences, said suppressed flow downstream of the Central Valley’s dams tends also to delay the outmigration of young salmon, which respond to high water as a trigger to move downstream. This delayed migration, he explained, threatens their survival in dry, warm years, when the longer a young salmon remains riverbound, the more likely it is to be eaten.
Climate change, Jeffres added, is exacerbating this problem.
“We’re seeing warmer water and poor migratory conditions occurring earlier and earlier,” he said.
In a 2018 paper, Michel and several colleagues concluded “that flow remains the single most influential factor for determining survival of late-fall Chinook salmon smolts outmigrating from California’s Central Valley.”
Who Doesn’t Love Salmon?
Flavorful and high in fat and protein, Chinook salmon appeal to a wide array of creatures, from trout feasting on eggs in headwater gravel beds to orcas consuming adult fish in the ocean. In the life stages in between, birds, mid-sized mammals, and many predatory fishes target Chinook. These include native species like Sacramento pikeminnow and hardhead but also nonnatives like striped bass and four species of black bass – largemouth, smallmouth, spotted and redeye.
Striped bass numbers have declined in recent decades, in tandem with native salmonids and, according to Rypel, likely due to similar ecosystem disruptions. This pattern, he said, distorts the notion that they are responsible for the state’s salmon decline.
“The conditions our native fish like are also the conditions striped bass like – colder water, more turbid water, access to wetlands,” said Rypel, who now directs the School of Fisheries, Aquaculture and Aquatic Sciences at Auburn University, in Alabama.
Black bass are another story. They thrive in conditions very different from those supportive of salmon (and striped bass), and their numbers have grown in California as Central Valley waterways have become warmer and clearer and generally more akin to Southeastern lakes and swamps where these fish evolved.
To better understand the impact these species may have on salmon, FishBio’s researchers sampled the Stanislaus River’s predatory fishes and inspected their stomach contents in the wet year of 2019 and the two following drought years of 2020 and 2021.
The scientists captured 1,770 black bass in the study’s course and 441 striped bass.
“Those voracious predators that inhabit the Delta and the rivers that flow into it are one of the main reasons less than 5% of the young salmon born in the Stanislaus River are estimated to survive their perilous journey each spring to the Pacific Ocean,” wrote the managers of the South San Joaquin and Oakdale irrigation districts, which funded the research, in a 2019 media release.
But the study would produce a more temperate conclusion. Averaged across the three years of sampling, just 4% of black bass and 17% of striped bass were confirmed to contain salmon in their stomachs at all, with a total of 242 salmon found in these species through the research term. Mostly, the bass contained items like mayflies, dragonflies, crayfish and other invertebrates.
FishBio’s scientists found that each predator group consumed Chinook salmon more frequently in the wet year than in the dry years, though not by a large margin – even though Chinook smolts were 10 to 30 times more abundant in the wet year than the study’s driest year, 2021. Ultimately, the population impact of predation on salmon was much lower in the wet year, though Lee believes FishBio’s diet analysis methods – visual identification, with DNA analysis ultimately underestimated actual predation.
Michel and several colleagues conducted a similar study, publishing results in 2018. Using DNA analysis of stomach contents, they found that, in the lower San Joaquin River, 2.8% of largemouth bass and 4.8% of striped bass sampled had eaten Chinook salmon.
The scientists noted that, even though few bass had eaten salmon, “predators could still be responsible for significant declines in the salmonid populations” simply due to the high numbers of bass in the Delta region.
Lee believes the black bass profusion in the Central Valley cannot be ignored.
“We have a world-class black bass fishery in the Delta, and that fishery is in direct conflict with the salmon fishery,” he said. He suggested “lifting all limits on black bass.”
Michel and his colleagues cautioned against such measures. That’s because they also found that nonnative predators frequently prey on other nonnative predators. While detecting cannibalism was impossible because of the analysis method (for example, every striped bass will test positive for striped bass DNA), they found that almost 30% of striped bass had eaten largemouth bass and 20% of largemouth bass had eaten striped bass. Channel catfish, they found, ate even larger numbers of both striped bass and black bass.
“Removing large numbers of one predator could release pressure on another predator population,” they wrote.
Jeffres pointed to another possible outcome of encouraging anglers to catch more nonnative bass: It could put people traditionally reliant on subsistence fishing – recreational anglers from low-income and disadvantaged communities – at risk of consuming dangerous levels of mercury, PFAS and other contaminants that bioaccumulate in predatory species.
“From a social justice perspective, I have a fundamental problem with that,” Jeffres said.
The 2007 Crash: Who Dunnit?
Gold mining and the construction of levees and dams, in the 19th and 20th centuries, had a heavy and lasting impact on historical salmon numbers, but the fish remained relatively abundant into the first years of the 21st century. Then, around 2007, their population went over a cliff. In the years since, salmon abundance has seen two spikes – one around 2013, the other in 2019. Neither lasted, but each occurred two to three years after a very wet winter.
Water supply advocates have said the 21st century Chinook downfall signals that restrictions on exporting Delta water are failing to revive the fish, and that predation is the biggest stone still unturned.
“We’ve tried everything else,” wrote Edward Ring, a frequent advocate for water supply and the cofounder of the California Policy Center, in a June, 2024 essay in the California Globe. “Remove all limits on bass fishing. Or just admit the bass won. Either way, restore water deliveries.”
But scientists say there’s more to this story. That’s because the extraordinary mid-aughts salmon collapse corresponded to extraordinary environmental conditions, including multiple periods of stalled ocean upwelling that starved the marine food web of nutrients and a pair of crushing droughts.
Moreover, dedicated environmental flows in recent years, scientists believe, have been inadequate.
“We can’t take flow off the table … because I don’t think we’ve given it an honest try yet,” Michel said. “There have been some fish-friendly water actions, but a lot of them have been too little, too late.”
Pulse flows, featuring small bursts of water released from dams specifically to flush salmon seaward, have become a management strategy, but they’ve only occurred in the last two years on the Sacramento River. Overall, the management of the Central Valley’s rivers has stripped them of the seasonal flow patterns that native fish “evolved with and adapted to centuries prior,” Michel said.
“We’ve homogenized flows downstream of dams and we’ve inverted the hydrograph, where we store water in the winter, spring and fall, when the fish typically would outmigrate, and instead we’re delivering much of the river downstream in the summer,” he said.
Rypel noted how water and reservoir management “has put the river in a perpetual state of drought” that tips the system into the favor of invasive predators.
There may be no single silver bullet solution to reviving the Central Valley’s salmon and other native species, but many scientists see a holistic attack strategy. Supported by research but fraught with political tension, it involves habitat restoration and more generous allocation of water to fish when they need it.
“It’s one of these inconvenient truths, because we need water for agriculture, for people, for cities,” Rypel said. “So, we don’t want to say that we’re taking too much water out of the river, but the science often points to the probability that we are.”
This story was produced by Estuary News Group with funding from the Delta Stewardship Council.
