Photo courtesy of the San Joaquin River Restoration Program.
After Friant Dam on the San Joaquin River was finished by the Bureau of Reclamation in 1944, the once huge run of Spring Chinook Salmon became extinct. The federal government, in violation of the Califorrnia Fish and Game Code, failed to construct a fish ladder or build a fish hatchery as mitigation for the loss of spawning grounds on the river.
Salmon returned to the river below Friant Dam for several years, but they had no way to get to where they once spawned and ended up dying in sloughs and canals and the run was no more. One CDFW biologist tried to save the remaining salmon before the run became extinct, but he received no support from state or federal authorities at the time.
But a group of anglers and environmentalists in the late 1980s began a movement to restore the run to river. Twenty years ago, as a result of a court settlement to a lawsuit, flows were mandated to once again flow in a section of the San Joaquin River.
Finally, the San Joaquin River Restoration Program that resulted from legal action and political pressure resulted in the reintroduction of spring-run juveniles in 2014. But since the native San Joaquin spring-run Chinook salmon had become extinct, those spring run juveniles had to be obtained from the Feather River Hatchery in Oroville, California.
In a year where the outlook looks increasingly dim for Sacramento River fall, winter and spring Chinook salmon because of massive water diversions from the Sacramento-San Joaquin River Delta and other factors, the San Joaquin River Restoration Program set a new record this year for returning adult spring-run Chinook salmon: 448. This is the highest number of captured returns recorded since the Program started reintroducing spring-run juveniles in 2014.
“The high return numbers clearly demonstrate that spring-run Chinook can survive and return to spawn in the San Joaquin River” said program manager, Dr. Donald Portz in a press release. “We look forward to a future where salmon will be able to swim unencumbered all the way to spawning grounds below Friant Dam.”
The previous record for captured natural returns was 93 set in 2021.
Due to multiple in-stream structures that halt their migration upstream, the San Joaquin’s returning spring-run Chinook must be captured in fyke traps – large-diameter, mesh cylinders placed in the river – before they are trucked in a tank approximately 120 miles to Reach 1 of the Restoration Area near Friant Dam and released, according to Portz.
“Our fish need the cooler water and habitat of Reach 1 in order to hold over the summer before they spawn in the fall,” said the Program’s lead fish biologist, Dr. Oliver “Towns” Burgess.
“While most of this year’s adults were caught in fyke traps located in the Eastside Bypass downstream of the State of California’s Eastside Bypass Control Structure, spring-run Chinook were also trapped and hauled from Sack Dam, about 45 miles upstream of the control structure. Earlier in March and April, higher river flows allowed salmon to get past the Eastside Bypass Control Structure and at least one got up to Sack Dam – the next in-stream impediment after the control structure,” according to Burgess.
“We expect to begin construction on the Arroyo Canal Fish Screen and Sack Dam Fish Passage Project at the end of the summer this year,” said Program Manager Portz. The project will allow fish to pass around Sack Dam and avoid diversion into Arroyo Canal.
“Installing a fish screen for Arroyo Canal will benefit both fish and farmers by protecting salmon from straying into canals while allowing water users to continue their lawful water use,” said Portz.
Portz said he also expects passage at the control structure to be completed by the same time passage at Sack Dam is completed in summer 2028. Currently, unless high river flows are present, returning adult salmon are unable to make their way past the control structure.
Spring-run Chinook salmon are anadromous, meaning that they begin their lifecycle in fresh water before migrating out to the ocean. There, juvenile salmon mature for several years in salt water before returning as adults to their natal rivers and streams to complete their lifecycle by spawning before they die.
But what does it take to get a high number of returning adults and grow a population of salmon?
“It is believed that the success of outmigrating juveniles is a key factor related to a higher number of returning adults. Salmon have evolved to account for boom/bust water years by adapting strategies to maximize survival in wetter years to compensate for poorer survival in drier years,” the program stated.
“For example, a certain percentage of juveniles — known as yearlings (see lifecycle illustration above) — stay in their natal fresh water for an additional year before emigrating to the ocean. This adaptation helps to support the generation if factors such as disease or drought take their toll. In other instances, a wetter year may encourage juveniles to move out of the system to the ocean more rapidly,” according to the program.
Burgess illustrated the point that high water years in 2017 and 2023 likely resulted in higher juvenile outmigration survival which led to larger adult returns two years later.
“We’re likely seeing a high-number of returning adults this year because of their successful exit as juveniles,” he said.
“In addition, the San Joaquin’s spring-run Chinook population are developing local adaptation to the San Joaquin Basin. This, in turn, can add diversity to the larger population of Central Valley spring-run Chinook salmon and increase their resiliency throughout the Central Valley — a concept known as the Portfolio Effect,” Burgess pointed out.
This isn’t the first time the Program has seen a high number of returning adults. 2017 was a high-water year on the San Joaquin River and in 2019, biologists estimated on the order of 400 returning adults to the San Joaquin, according to Burgess. An exact number is unknown since field crews had to curtail monitoring due to flood conditions. However, over 200 redds (fish nests) were counted in the river.
“Given the record-high number of returns this year, we’re hopeful that we surpass the 2019 record for redds this fall,” added Burgess.
Return spring-run monitoring for this year concluded on June 5. As is their lifecycle, the salmon currently in the river will hold in Reach 1 until September when spawning will commence, with the emerging generation expected in November before outmigrating to the ocean in spring 2026.
The record return of Spring Chinook Salmon in the San Joaquin River Restoration Program shows you that salmon can be definitely return to a river where they have been extirpated for decades.
Unfortunately, due to state and federal water and management policies, combined with the impacts of climate change, pollution and warming ocean conditions, the situation with salmon in the Central Valley looks extremely bleak unless major action is taken by the state and federal governments.
The San Francisco Bay-Delta estuary is currently in its worst-ever crisis, as evidenced by the closure of commercial salmon fishing off the California Coast for an unprecedented third year in a row, due to the collapse of the Sacramento and Klamath River Fall Chinook Salmon populations. Meanwhile, Sacramento River Spring Chinook and Winter Chinook Salmon — listed under both the state and federal endangered species acts — continue to decline.
Yet the Delta Tunnel, Sites Reservoir and voluntary agreements promoted by Governor Gavin Newsom will only make the ecological crisis in the Delta even worse, since they will result in the diversion of even more water out of the Sacramento River before it flows through the Delta — when what the fish and ecosystem need is reduced water exports out of the estuary to agribusiness and Southern California water agencies.
The testimony of DWR engineer Amardeep Singh reveals that the Delta Conveyance Project (DCP) will increase water deliveries from the Delta by 22%, according to an analysis by the California Water Impact Network (C-WIN).
The data from the Pacific Fishery Management Council (PFMC) documents the abysmal situation that Sacramento River Fall Chinook Salmon, once the driver of the West Coast salmon fishery, and the Spring and Winter Chinook are now in.
Between 1996-2005 the average return for fall-run Chinook on the mainstem Sacramento River was 79,841 spawning salmon. In 2023 that number fell drastically to only 3,560 salmon – a 95% decline, according to an analysis by the Golden State Salmon Association.
Spring-run Chinook have also experienced a staggering 95% decline due to a lack of cold water flows in Central Valley salmon rivers. The average wild and hatchery spring-run return plummeted from 28,238 fish in 2021 to just 1,231 salmon in 2023.
And spawner escapement in 2024 of endangered Sacramento River Winter Chinook, an endangered species under both the state and federal Endangered Species Acts, was estimated to be only 789 adults and 578 jacks (two-year-olds).
This number of Winter Chinooks is just a fraction of the millions that returned to the Sacramento River system to spawn historically. Even after the Shasta Dam was built, 117,000 Winter Chinooks retuned from the ocean to spawn in the Sacramento River below Shasta and Keswick dams in 1969.
Delta Smelt is functionally extinct in the wild
It’s crucial in understanding how bad the situation is in the once robust Bay-Delta estuary to review the current status of Delta Smelt and other pelagic species on the Sacramento-San Joaquin River Delta.
For the seventh year in a row, the California Department of Fish and Wildlife CDFW found no Delta Smelt in the California Department of Fish and Wildlife’s Fall Midwater Trawl Survey in the Sacramento-San Joaquin River Delta in 2024. This 2 to 3 inch fish is an indicator species that has been villainized by Donald Trump and his corporate agribusiness allies for supposedly being a “worthless fish,”
It is significant that zero Delta smelt were caught in the survey despite the release of tens of thousands of hatchery-raised Delta smelt into the Delta over the past few years by the state and federal governments.
“The 2024 abundance index was 0 and continues the trend of no catch in the FMWT since 2017,” reported Taylor Rohlin, CDFW Environmental Scientist Bay Delta Region in a Jan. 2 memo to Erin Chappell, Regional Manager Bay Delta Region: nrm.dfg.ca.gov/...
“No Delta Smelt were collected from any stations during our survey months of September-December. While FMWT did not catch any Delta Smelt, it does not mean there were no smelt present, but the numbers are very low and below the effective detection threshold by most sampling methods,” she wrote.
The CDFW has conducted the Fall Midwater Trawl Survey (FMWT) to index the fall abundance of pelagic (open water) fishes annually since 1967 (except 1974 and 1979), Rohlin stated.
Other surveys last year also reveal the functional extinction of Delta smelt in the wild. A weekly survey by the US Fish and Wildlife Service targeting Delta smelt caught only one smelt in the summer of 2024. “A late April IEP juvenile fish survey (the 20-mm Survey) caught several juvenile Delta smelt in the same area,” noted scientist Tom Cannon in his blog on the California Sportfishing Protection Alliance website: calsport.org/...
The Delta Smelt is a key indicator species that demonstrates the health of the Sacramento-San Joaquin River Delta, the largest estuary on the West Coast of the Americas. The 2 to 3 inch fish that smells like a cucumber is found only in the Delta.
It was once the most abundant fish in the Delta, numbering in the millions, but now is functionally extinct in the wild due to massive water exports to agribusiness and other factors, including invasive species, toxics and pollution, over the past several decades.
The significance of the Delta smelt’s role in the Bay-Delta Estuary cannot be overstated.
”Delta Smelt are the thread that ties the Delta together with the river system,” said Caleen Sisk, Chief of the Winnemem Wintu Tribe. “We all should understand how that affects all the water systems in the state. They are the irreplaceable thread that holds the Delta system together with Chinook salmon.”
Other pelagic fish species are in free-fall also
The other fish species collected in the fall survey — striped bass, longfin smelt, Sacramento splittail and threadfin shad — continued their dramatic decline since 1967 when the State Water Project went into effect. Only the threadfin shad showed an increase from the last year’s index — and the population is still at just a fraction of its former abundance.
The survey uses an “abundance index,” a relative measure of abundance, to document general patterns in population change.
The 2024 abundance index for striped bass, an introduced gamefish, was 136, representing a 49% decrease from last year’s index.
The index was 175 for longfin smelt, a native fish species, representing a 62% decrease from last year’s index.
The index was 577 for threadfin shad, an introduced forage fish, representing a 12% increase from last year’s index.
The index for American shad, an introduced gamefish, was 1341, representing a 45% decrease from last year’s index.
The index for Sacramento splittail, a native minnow species, was 0, with 0 fish caught.
To put things truly In perspective, one must understand that these substantial decreases were from already abysmally low levels of abundance.
Between 1967 and 2020, the state’s Fall Midwater Trawl abundance indices for striped bass, Delta smelt, longfin smelt, American shad, splittail and threadfin shad have declined by 99.7, 100, 99.96, 67.9, 100, and 95%, respectively, according to the California Sportfishing Protection Alliance.
The graphs in this CDFW memo graphically illustrate how dramatic the declines in fish populations have been over the years: nrm.dfg.ca.gov/…
