Overview:
Important projects are underway to bring salmon runs back to the San Joaquin River below Friant Dam, two decades after a 2006 legal settlement made it possible.
It’s salmon squeezing time at California’s newest, most technologically-advanced fish hatchery.
Standing in a large tank filled with 54 degree water, a fish technician passes an ultrasound wand across the abdomen of an adult female Chinook salmon to ensure its eggs are fully developed.
If so, techs then squeeze out some eggs from the salmon’s belly while feeling for the looseness of the remaining eggs. Each ripe female is then transported into a separate holding tank for spawning the following day.
Male broodstock get similar handling, except the squeezing is employed to express milk. The males also get scanned (via a transponder tag embedded in their abdomen) to determine which are the least genetically related to the females.
Why? Because the last thing biologists want, especially when resurrecting a salmon run that was killed off for more than six decades, is inbred fish.
“Genetic diversity is really important in a population because it gives the population the ability to adapt to changing conditions in the river,” explained Brian Erlandsen, a senior environmental scientist supervisor for the California Department of Fish and Wildlife. “So you try to maximize that as much as you can.”
Opened in May 2025 along the San Joaquin River in the town of Friant, just outside Fresno, the Salmon Conservation and Research Facility produces spring-run Chinook salmon expressly for the San Joaquin River Restoration Program.
Made up of five federal and state government agencies, the Friant Water Users Authority, exchange contractors and environmental organizations, the San Joaquin River Restoration Program (SJRRP) is the result of a 2006 legal settlement that followed an 18-year lawsuit over California’s second-longest river.
Its purpose: To bring back a once-mighty salmon run, the southernmost in the state, which went belly up when the completion of Friant Dam in 1942 virtually dried up a 150-mile stretch of the San Joaquin River from the dam down to the Merced River confluence.
Salmon are anadromous fish, meaning they live in both fresh and salt water and travel up and down river systems during their life cycle. Born in fresh water, juveniles migrate to the ocean to mature then return as adults to their native streams to spawn and die.
A robust salmon run
Before Friant Dam, an estimated 200,000 to 500,000 adult Chinook salmon returned to the San Joaquin River each year. The runs were said to be so dense that inhabitants who lived nearby were kept awake at night by the sound of fish splashing their way upstream.
Today, the only evidence of this former abundance exists in old photographs such as those displayed at Scout Island in northwest Fresno.
“People used to pitchfork the salmon, fill up barges with fish and bring them down the river to San Francisco and sell them in the fish market,” said Don Portz, a Bureau of Reclamation fish biologist who serves as SJRRP program manager. “I mean just crazy stuff.”
The SJRRP operates under two co-equal goals designed to balance ecological recovery with regional economic stability: Restore and maintain a self-sustaining population of spring-run Chinook salmon — but do so in a manner that does not adversely impact farmers that rely on water from the river and stored in Millerton Lake.
Due to a variety of factors, not the least of which were severe droughts from 2007-09, 2012-16 and 2020-22 that reduced recovery flows in the river, program managers are well behind the timeline established by the 2006 settlement.
Still, there has been progress. The SJRRP reached a milestone in the summer of 2025 when 448 adult spring-run Chinook salmon returned to the river — the highest number by far since juveniles were first reintroduced in 2014.
Most of those 448 returning adults were released as juveniles in 2023 and likely benefitted from high flows caused by flood releases from Friant Dam during their out-migration period, CDFW spokesperson Krysten Kellum said. This year, by comparison, just 54 adult salmon returned to the river out of the roughly 220,000 juveniles released in 2024’s drier conditions.
Blockages impede salmon
Despite increased flows mandated by the settlement, salmon are prevented by structural blockages from swimming unencumbered up and down the river system.
Each early spring, juvenile salmon raised at the $44 million state bond-funded hatchery are transported by truck and released at the Merced River confluence near Newman.
The Salmon Conservation and Research Facility will produce roughly 250,000 juveniles for release next spring but has capacity for up to 1 million. In summer, returning adults are captured in long, cylindrical nets at multiple locations and trucked to Fresno, where they swim upriver to spawning beds below the dam.
To allow the fish to migrate freely along a river system that has been altered significantly since historical times, four major passage impediment projects must be completed.
The first is currently underway east of Dos Palos. Construction of a bypass channel that will reroute the river around Sack Dam and the Arroyo Canal began in 2025. When finished, adult salmon will be able to swim upstream via a ladder and ramp during normal and higher flows while juveniles moving downstream will be able to pass through a control structure.
The Bureau of Reclamation awarded a $93 million contract for that project but actual costs could exceed $100 million, Portz said.
“What we are doing out there is truly an amazing feat,” Portz added. “If you look at the size of that project alone, I don’t know of another project in California of that size that is for water conveyance and fisheries protection in one lump.”
A significantly larger amount of federal funding — perhaps as much as $700 million — will be required near Mendota, where there are plans to build a half-mile channel around Mendota Pool with levees capable of withstanding flood-level flows. Other components include a fish ladder and screen, reverse flow facility, a fish recapture facility and a new south-end dam.
Senator requests extra $500 million
To fully fund the Mendota Pool bypass project, Senator Alex Padilla (D-California) introduced a bill that would allocate an additional $500 million to the SJRRP. The Senate Committee on Energy and Natural Resources advanced the bill in July; it awaits a full floor vote.
Work on the Mendota Pool bypass is expected to begin in 2028, Portz said, following completion of the Sack Dam and Arroyo Canal project.
The two other passage impediment projects, improving fish passages at the Eastside Bypass Control Structure and Chowchilla Bifurcation, are purview of the California Department of Water Resources. Funding for both has been approved.
Other factors that have hampered salmon restoration efforts include low flows during drought years and, to a lesser extent, seepage into adjacent orchards and predation by bass and other nonnative fish.
Portz, who has managed the SJRPP since 2018, estimated it would take until 2035 for the river system to be completely navigable by salmon during normal and wet years. Which, he acknowledged, is well outside the timeline contained in the 2006 settlement. Restoration flows were supposed to have occurred by 2014.
“However, if you took and you truly look at what it takes to bring back a river from a dry, sandy, barren river channel to reconstituting water and bringing back an extirpated species, I’d say we’re doing pretty darn good right now and gaining steam,” Portz said.
This story was produced by the Climate Solutions Studio, a project of the Central Valley Journalism Collaborative and its partner newsrooms.
