Estuary News

October 2022

The Long Haul to Restore San Joaquin Spring-Run Chinook

When a team of fish biologists was tasked with restoring spring-run Chinook salmon in the San Joaquin River in 2006, none of them quite knew where to begin. The thirsty farms that crowd the river on both sides had taken almost all the water out of it most years since the mid-1900s, leaving a nearly 60-mile long stretch below Friant Dam near Fresno completely dry. The riverbed had been parched for so long that someone even built a house in it. The salmon that once thronged up-river by the hundreds of thousands had vanished, and there was no precedent for jumpstarting a population from scratch.

Then one of the team members joked that they should just write a white paper saying it wasn’t going to work. “That broke the tension,” recalls Gerald Hatler, who manages the California Department of Fish and Wildlife’s Central Region Fisheries Program. “We all laughed—and then we sharpened our pencils and got to work.”

That was shortly after a Natural Resources Defense Council (NRDC)-led coalition prevailed in its 18-year lawsuit against the Friant Water Users and the U.S. Department of the Interior seeking to restore threatened spring-run Chinook and other fish in the San Joaquin River. The settlement guaranteed water releases of up to 4,500 cubic feet per second for fish from Friant Dam and established the San Joaquin River Restoration Program, which is charged with restoring a naturally spawning, self-sustaining population of 30,000 spring-run Chinook while minimizing adverse impacts on agriculture and other water users.

The restoration program, which launched in October 2009, is a mix of spectacular success and drawn-out delays. Adult spring-run Chinook from test releases of young are already returning to the San Joaquin River after their decades-long absence. But key settlement target dates for officially reintroducing salmon and reestablishing fish passage by 2012, and releasing full restoration flows by 2014 have come and gone. Now, the program is finally on the cusp of major milestones on both the reintroduction and passage sides. The timeline for full restoration flows, however, remains uncertain.

Spring-run have a distinctive life cycle among Chinook. “Fall-run come up in the fall, spawn, and die,” Hatler says. “Spring-run come up in the spring and stay the summer.” The San Joaquin River used to be perfect for summering adult spring-run. The river starts near the crest of the Sierra Nevada; salmon would shoot upstream as high as 3,300 feet, where snowmelt kept the water cool in deep pools that sheltered these three-foot, 30-pound fish through the summer. Historically the San Joaquin River’s spring run was one of the largest Chinook runs on the Pacific Coast with as many as one million returning as adults every year, according to California Trout.

Image: U.S. Bureau of Reclamation.

Today the San Joaquin River has 27 dams, six reservoirs, and nine hydropower plants along its 366 miles, making it among the most heavily dammed and diverted rivers in California. It’s all but impossible for fish to swim up the river. Salmon can only migrate to their remaining spawning grounds below Friant Dam in the wettest years, when the river runs at its highest. Most years the fish only make it as far as the San Joaquin River’s confluence with the Merced River. The restoration program focuses on the usually inaccessible 152 mile stretch between the Merced River confluence and the 319-foot Friant Dam.

Although spring-run Chinook were long gone from the San Joaquin River when Hatler and his fellow fish biologists set out to restore them, there were still a few small populations in the Sacramento River. So the team decided to pool fish from those remnant populations and raise their young in a new conservation hatchery near Friant Dam. “We wanted to increase the genetic diversity so we could get a population uniquely adapted to the San Joaquin River,” Hatler says. The conservation hatchery has been much delayed by construction troubles but is now on track to be operational in 2023, capable of producing upwards of one million young spring-run Chinook annually.

In the meantime, the restoration program began test releases of young spring-run from the Feather River Hatchery in 2014, starting with 60,000 and now exceeding 200,000 per year. These releases are experimental, designed not to restore the population but rather to inform the eventual large-scale reintroduction of conservation hatchery fish. So it was a thrill when these experiments had the  remarkable result of producing 23 spring-run Chinook that completed their lifecycle and made it back to the San Joaquin River to spawn in 2019. Spring-run have continued to come back every year since, with 57 adults returning in 2020, 93 in 2021, and 11 in 2022.

“When I first got involved, I had a healthy amount of skepticism,” Hatler says. “I’ve been pleasantly surprised.” But his shift toward optimism is tempered by the fact that in all but the wettest years salmon still can’t make it to the spawning grounds themselves. “We have to put them there,” he continues. “Adults that come up the river get stuck well before Friant Dam so we truck them the rest of the way.”

Even though they often need trucking, it’s amazing that spring-run Chinook have begun returning to the San Joaquin River at all. “People were kind of shocked—we weren’t expecting them to come back yet,” says Trout Unlimited California science director Rene Henery, who has served on the restoration program’s Technical Advisory Committee for a decade.

The odds against the salmon seemed too great. The experimental releases are quite small, fish get a mere trickle of the restoration flows they were promised in the settlement, and there are still major barriers to adult migration.

Hatchery-raised juvenile spring-run Chinook salmon are released at the Fremont Ford State Recreation Area. Photo: U.S. Bureau of Reclamation/Josh Newcom.

Donald Portz is doing his best to change that. “Wet years are few and far between,” says Portz, who has been with the San Joaquin River Restoration Program almost since the beginning, first as the fish biologist and now as the program manager. “We need to improve passage in normal and dry years.” In the driest years, adults will still need to be trucked upstream even after fish passage is improved.

Salmon swimming upriver run into three major barriers, which are at 18, 64, and 86 miles past the Merced River confluence. The first is a five-foot vertical drop at the downstream end of the Eastside Bypass, part of a 52-mile flood-control channel that conveys excess water from the San Joaquin River during very wet years. Water sheets down this drop too fast for salmon to withstand; the fix includes building a rock “ramp” that salmon can climb.

Next comes the nine-foot Sack Dam. Here, the fix includes bypassing the dam with a fishway designed to mimic a natural river channel. This project has been held up because the land around Sack Dam is sinking so fast due to groundwater pumping that it’s literally a moving target. “It’s very hard to come up with a design that will work with high subsidence for years to come,” Portz explains, adding that program engineers think they’ve finally done it.

The last major obstacle is the 23-foot Mendota Dam and the adjacent Mendota Pool, a water-delivery hub with diversion channels radiating from it like spokes on a bicycle wheel. The channels are hazards for salmon, which can get diverted along with the water. This fix is more complex and includes a fishway around the dam as well as setback levees around the pool, which will create more than 800 acres of floodplain nurseries for young salmon migrating downstream toward the ocean.

While Portz initially intended to stagger these three fish passage projects, he now expects them all to be complete in 2026. This will allow salmon to swim the entire length of the restoration area in all but the driest of years. But for that, of course, they also need water.

Restoration flows are limited by factors the settlement didn’t account for, such as seepage from the San Joaquin River into the almond and pistachio orchards planted in its former floodplains. Seepage can raise the water table, making soil too soggy or salty for these high-value crops.

This unforeseen consequence of restoring flows to the long-dry river has also delayed fixing the barriers to salmon migration. “Fish passage improvements were supposed to be the biggest expenditure, but the biggest expenditure to date has been buying seepage easements,” says Doug Obegi, NRDC’s director of California River Restoration. “These limits on restoration flows to prevent naturally occurring seepage is wasting taxpayer money—it’s the biggest impediment to the success of the program.”

The program is also hampered by the region’s frontier mentality towards water. “It’s still quite a bit like the Wild West on the San Joaquin River,” Obegi says. People reportedly carry shotguns while adjusting valves, and agricultural water rights are fiercely defended.

Take the San Joaquin River Exchange Contractors Water Authority, called Exchange Contractors for short, which has some of the oldest water rights in the state and whose mission statement includes “maximize local water supply.” When Friant Dam was constructed in 1942, nearly one-quarter million acres of farmland on the west side of the valley could no longer draw water from the San Joaquin River. In exchange, west side farmers were allocated water from the Sacramento River via the Delta.

SJR Restoration Program Flow Schedule. Image: U.S. Bureau of Reclamation.

The catch is that when the Exchange Contractors are shorted on water from the Sacramento River, they make up the difference by reverting to their former water rights from the San Joaquin River. And the Exchange Contractors are not part of the restoration settlement, so they get this water at the expense of fish.

NRDC wants this exchange contract to be renegotiated. “In six of the past 10 years the Bureau of Reclamation has allocated as much or more water to the San Joaquin River Exchange Contractors than the entire flow of the San Joaquin River,” NRDC wrote in May 2022 letter to the Bureau. “In several recent years (2014 and 2022) the San Joaquin River has been dewatered and dried up as a result of water deliveries from Friant Dam to the Exchange Contractors.”

Exchange Contractors’ releases are a double whammy for spring-run Chinook in the San Joaquin River. Besides decreasing the water available to salmon, these releases are drawn from the bottom of the reservoir behind Friant Dam and so deplete the coldest water. Adult spring-run need this cold water to survive the Central Valley’s intense hot season.

These days most Central Valley Chinook are fall-run. But there used to be as many spring-run as fall-run, and the commercial fishery for the former once surpassed that of latter, with the California Fish Commission reporting catches of 567,000 and 213,400, respectively, in 1883.

But even though salmon fishermen once depended on Central Valley water for their livelihoods as much as farmers did, they were left out of the equation when people divvied up San Joaquin River flows. “When decision-makers replumbed the San Joaquin Valley to suit agricultural interests, salmon fishermen lacked political muscle,” says John McManus, president of the Golden State Salmon Association. “We’re living with the legacy of that to this day.”

The success of the San Joaquin River restoration will depend on whether the salmon ever get the water they were promised in the settlement. “We’ve shown the naysayers that it is very much possible to bring back this population,” Portz  says. “But you’ve got to have water.” If they get it, says Trout Unlimited’s Henery, “Spring-run Chinook are totally recoverable in the San Joaquin River. There’s tons and tons of reason for hope.”

Top: Friant Dam. Image: California Department of Water Resources.

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About the author

Robin Meadows is an independent science journalist in the San Francisco Bay Area. She covers water and climate change adaptation for Estuary News, is the water reporter for the Bay Area Monitor, and contributes to Bay Nature, Frontiers in Ecology and the Environment, PLOS Research News and Water Deeply. Robin also enjoys hiking and photography.

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