San Joaquin River salmon make big gains, but don’t call it a comeback yet

Fish biologists bringing back salmon runs on the San Joaquin River say a record number of fish nests have been found in the river below Friant Dam east of Fresno.

The number of nests, called redds, created by spring-run Chinook salmon reached 41 this year, compared to just 13 last year.

“It’s a vast improvement over previous years,” said fish biologist Don Portz, manager of the San Joaquin River Restoration Program. “That’s triple the amount.”

The numbers are encouraging to fish scientists because they show the restoration program is making progress in re-establishing a wild salmon fishery on the San Joaquin after six decades of absence. But there’s a lot of work to do before scientists can say they’ve done all they can.

“Right now we’re in the infancy stages of bringing the fish back,” Portz said.

Andreas Raisch, U.S. Fish and Wildlife Service biological science technician, far left, with Adriana Arrambide, scientific aide at California Department of Fish and Wildlife, work to make a flat bed for an emergence trap in the San Joaquin River at Friant. They are placing the trap over a redd - a nest of gravel where female salmon lay eggs - to catch newly hatched Chinook salmon for study during a salmon fishery restoration project, Monday morning, Nov. 19, 2018. In the background right, Emily Shaw, California Department of Fish and Wildlife scientific aide, and Austin Demarest, biological science technician, U.S. Fish and Wildlife Service, work to secure their side in the chilly water. JOHN WALKER jwalker@fresnobee.com

Last year, for the first time in 60 years, spring-run Chinook salmon successfully reproduced in the river, which made headlines.

To monitor the fish after they hatch, biologists are installing special nets, called emergence traps, directly on top of nine redds. The nets are designed to catch, but not kill, emerging salmon fry.

So far this year, no salmon fry have been found, but it’s early yet. It takes a couple of weeks for fish to hatch and a lot depends on water temperature. But when they appear, experts will count them, weigh them, measure them and test for genetics.

“I think it’s incredibly rewarding work to see how the fish are actually thriving in the sections of the river we are working on,” said fish biologist Stephanie Durkacz, who donned waders and installed several traps over the past two weeks. “There haven’t been spring-run chinook salmon spawning here in 60 years. ... It feels very historic.”

Turning the ‘spigot’ back on

The work is being done because an agreement with environmentalists requires the federal government to restore the lost salmon runs. A long stretch of the San Joaquin River dried up and with it the salmon when Friant Dam was built in the 1940s.

Stephanie Durkacz, fish biologist at US Fish and Wildlife Service, uses an instrument to gauge water conditions in the San Joaquin River at Friant, where an emergence trap was placed over a redd - a nest made of gravel where female salmon lay eggs - to catch newly hatched Chinook salmon for study during the river restoration project, Monday morning, Nov. 19, 2018. At center, Adriana Arrambide, scientific aide for California Department of Fish and Wildlife, moves in to secure the trap. JOHN WALKER jwalker@fresnobee.com

Several fish biologists, lawyers and members of the public recently toured the river with the Water Education Foundation, based in Sacramento. Portz, the river restoration program manager for the Bureau of Reclamation, laid out the stakes.

“This is a river that didn’t have flows for over half a century,” Portz said. “It’s not an easy thing to turn on the spigot and let water start flowing again.”

But hatchery-raised adult salmon released into the San Joaquin River are making redds and spawning, giving fish scientists hope for success.

A major goal of the restoration program is for salmon eggs laid naturally in the river to hatch and for juvenile salmon to swim to the ocean, reach sexual maturity, then return as adult salmon to spawn and die — and for the cycle to start all over again as it did for time immemorial.

That’s how it was until Friant Dam blocked the river in 1948 and the water stored in Millerton Lake was diverted to farms on the Valley’s east side as part of the federal Central Valley Project.

But under California fish and game code, dams must release enough water to keep fish alive downstream.

In 1988, the Natural Resources Defense Council sued the U.S. Bureau of Reclamation, which controls the dam, and all of the irrigation districts that use the water for farming. A federal judge sided with the NRDC.

At the judge’s urging, the parties in 2006 hammered out the San Joaquin River settlement mandating that both spring and fall salmon runs be restored, from Friant Dam to the confluence of the Merced River a distance of 153 miles.

Seeking a self-sustaining salmon population

There are two kinds of salmon in the San Joaquin River — fall run and spring run salmon.

Spring run salmon evolved to take advantage of spring pulses of snowmelt rushing down from the Sierra Nevada. Historically, the fish swam up from the ocean and lived in deep pools of cool water during the summer, then spawned in the fall.

By contrast, fall run salmon arrived in late November to early December and quickly spawned. Both spring run and fall run juveniles swim to the ocean in the late winter and spring.

“If you can’t bring them both back, we’re supposed to focus on the spring run,” Portz said.

Tagged juvenile spring run Chinook salmon swim in a tank at the Salmon Incubation and Rearing Facility near Friant Dam on Jan. 26, 2018. Tagging helps biologists monitor spring run Chinook salmon numbers as part of the San Joaquin River Restoration Program. CRAIG KOHLRUSS ckohlruss@fresnobee.com

The fish that hatched in the river late last year are spring run salmon. It was considered a major milestone.

The work has been slow to ramp up, but Portz says they’ll have all the necessary work completed by the end of 2024 so both spring and fall run salmon can swim unimpeded from the ocean to Friant Dam.

The Natural Resources Defense Council is keeping a close watch on developments.

“Progress is slower than required, and that is disappointing,” said NRDC lawyer Doug Obegi in an interview with The Bee. Still, he said, “we should have a fully functioning river, and that’s encouraging ”

The effort is funded by state and federal governments. Eastside farmers pay a “Friant surcharge” for their irrigation water, and the collected funds, about $8 million a year on average, is paid to the federal government.

Portz said the original cost estimate for the restoration work was $1.5 billion to $1.6 billion, but program managers gave the budget a “haircut” to cut costs. “It still came to $648 million for just phase one,” he said.

Costs include a new fish hatchery near Friant Dam, which is behind schedule but should open next year. The hatchery will eventually produce 1 million salmon fingerlings annually. An interim hatchery on the river now produces 200,000 fish per year.

The hatchery is needed because naturally producing salmon on the river won’t be enough to restore the salmon runs, at least at first.

“We want a naturally reproducing, self-sustaining population, but you need a supplement,” Portz said.

The long-term goal is to have tens of thousands of returning salmon — 10,000 fall run and 30,000 spring run.

This year, 168,000 juvenile hatchery fish were released into the river and last year it was about 150,000. Similar numbers have been released since 2014. It takes two or three years for them to return as adults.

What’s the next milestone?

So far, returning adult Chinook salmon have not yet been seen in the San Joaquin River. But Portz and the other scientists have their fingers crossed that salmon will start showing up on the San Joaquin next spring.

When that happens, “the returning adult spring run salmon will be the next milestone for the program,” he said.

Because of physical barriers still in the river that stop the migrating fish, the fish will be netted downstream and trucked to the waters below Friant Dam, he said.

There currently isn’t enough water in the river to support a fully functioning salmon fishery, Portz said. Levees will be built where needed so the channel can contain more water, he said.

Andreas Raisch, U.S. Fish and Wildlife Service biological science technician, left front, and others carry an emergence trap to lay in the chilly water of the San Joaquin River at Friant and place it over a redd to catch newly hatched Chinook salmon for study during the river restoration project, Monday morning, Nov. 19, 2018. JOHN WALKER jwalker@fresnobee.com

There’s also a need to build “fish passages,” man-made structures allowing fish to swim around dams and get upriver on their own, which biologists call “volitional passage.” The fish passages will be built by 2024 as required by the settlement, Portz said.

But it’s water temperature that is the crucial factor for salmon survival, he said, especially for juvenile fish going out to the ocean. That’s why cool water at the bottom of Millerton Lake must be sent downriver.

“We have to time our releases effectively,” Portz said. “We need to have planned pulses to move the juvenile fish and start their migration to the ocean.”

The settlement requires water in the river all year long. That leaves less irrigation water for farmers — about 15 percent to 20 percent less per year on average than before the settlement.

But the farmers are banking on there being no more reductions and support bringing back salmon on the river.

“Friant Water Authority continues to be invested in the long-term success of the San Joaquin River Restoration Settlement and program,” the water delivery agency said in a statement. “We believe the terms of the settlement were fair and we’re working with our partners to fully implement it.”

One major unknown, meanwhile, is the effect of climate change on the San Joaquin River salmon. Spring run salmon would probably do better than fall run salmon in an era of global warming, Portz said.

“Because they spawn earlier in the fall, they move out earlier in the year: February, March, into April,” he said. “Water temperatures are still cool.”

But it means managers must make the right calls so the adult salmon will return despite climate change, he said.

“People are going to say, ‘This can’t be done,’ ” Portz said. “But if we do our fish passage right, and provide the habitat that’s necessary, I think it is attainable.”

Other work includes creating rearing habitat for salmon, adding screens to keep fish from migrating into side channels where they would get stranded, and building a fish screen, to be the largest in the state, to keep salmon out of Mendota Pool on the Valley floor.

Additionally, more gravel must be put in the river so returning adult fish can create their redds.

Lewis Griswold: 559-441-6104, @fb_LewGriswold