It’s easy to see how biologists studying the fate of California’s native fish might fall into despair. That’s how Jacob Katz felt when he and his colleagues reported in 2011 that more than three-quarters of the state’s native freshwater fish, including its iconic Chinook salmon, were in sharp decline. 

But Katz, a fly-fishing ecologist who directs Central Valley operations for the conservation nonprofit California Trout, isn’t the despairing type. His eyes lit up as he recalled the moment he realized the same forces leading California’s fish to the brink of extinction could be harnessed to reel them back. 

That epiphany now drives his work. Restoration isn’t about removing any one dam or returning to some mythical pristine condition but about helping salmon recognize the rivers they evolved with, said Katz, walking along a flood-protection levee that cuts off the Sacramento River, California’s longest, from the thousands of farms and towns that occupy its historic floodplains. When you realize “farms or fish” is a false choice, he said, “suddenly you see that you can have both.”

California’s labyrinthine system of dams and levees cut off once roaring rivers from millions of acres of their floodplains, drastically reducing the habitat and food salmon need to thrive. Climate change may hasten extinctions by raising water temperatures and disrupting flows with bigger floods and more frequent and severe droughts, which also threaten to reignite conflicts over increasingly scarce water. 

But such dire prospects have inspired a novel alliance in one of the most productive agricultural valleys in the country, which has turned adversaries into allies to offer salmon and other threatened wildlife a lifeline.

Farmers in the Sacramento Valley have partnered with biologists, water regulators and conservation groups to imagine “a new way forward” to restore wild fish runs. They aim to create what Katz calls a “string of pearls” along the Sacramento River by reconnecting the highly leveed waterway with its floodplains at places most likely to benefit fish. 

That might involve adding gates to weirs that open so young salmon can move in and out of fields or pumping fish food into rivers. If the plan succeeds, it will turn the same fields that grow rice for people in the summer into rearing habitat and food factories for young salmon during the winter, increasing their odds of reaching the ocean and, ultimately, returning to spawn. 

“Salmon need unimpeded migration corridors, both as juveniles and adults, and the ability to migrate thousands of miles in the ocean and come back,” said Robin Waples, a senior scientist at the National Oceanic and Atmospheric Administration’s Northwest Fisheries Science Center whose pioneering work on the population genetics of salmon led to listing Pacific salmon species as endangered.

But just about everything people do related to urbanization, agriculture, forestry and road building harm salmon, Waples said. All have conspired to make one of nature’s most improbable migrations nearly impossible. 

Before settlers dammed the valley’s rivers and drained its marshes, a dynamic mosaic of seasonal wetlands and riparian forests supported millions of salmon that fed wolves, grizzlies and bald eagles that once inhabited much of the state. Every year rivers swelled with winter rains and spring snowmelt, overflowing their banks and spreading out slowly across the floodplains. 

“We drained the entire valley at a time when we didn’t realize the water’s importance for fish and birds,” said Roger Cornwell, who works with Katz as manager of River Garden Farms, which grows rice, wheat and other crops on 15,000 acres northwest of Sacramento in Knights Landing. “Once you disconnected the land and the water, that really changed things. Now we’re starting to understand that there’s a great opportunity to reverse that.”

That involves redrawing old battle lines that pit farmers against fish to find ways to restore key elements of the valley’s hydrological history in a way that benefits both people and native species. They aim to do that by harnessing an emerging understanding of how fish once used rivers and seasonal wetlands during key stages in their life cycle. 

Once you understand how dams and levees interrupted the ecological processes embedded in rivers and wetlands, Katz said, it’s possible to integrate those processes into managing farms, ranches and other working landscapes.

“It’s not an inevitable consequence of human development that you have endangered fish populations,” said Katz. “It’s a direct result of infrastructure, built at a time when we knew little about how rivers worked or how fish use them.” 

Making Up for Past Mistakes

California’s salmon were already facing steep declines from overfishing and habitat degradation caused by mining runoff in the early 20th century. 

With no limits on catch at the time, fisherman routinely tossed gill nets across rivers, said Ron Yoshiyama, a salmon biologist and historian affiliated with the University of California, Davis. “That pretty much stopped spawners from getting up to their spawning grounds.”

Yet state officials looked for other reasons to explain low numbers of fish in the river. In 1911, a Fish Commission employee named Norman Scofield led an expedition into the Sacramento’s flood basins “to improve on nature” by propagating fish in hatcheries. Scofield visited the basins in the middle of April, even though he acknowledged that flooding usually peaked toward the end of February. 

He saw vast numbers of juvenile salmon on the floodplains and assumed it was a death trap, not realizing the vast majority had already made their way back to the river. Even then, levees had destroyed many of the channels that juveniles likely used to get back to the river, Yoshiyama said. “That misled a lot of people into thinking that floodplains were bad. But work from the Department of Water Resources and Jacob’s work with them have demonstrated that flood plains are, in fact, a key feature of their life history.”

And following the law of unintended consequences, Chinook raised in hatcheries now threaten the survival of dwindling wild populations. Fall run Chinook hatchery populations are the Central Valley’s most abundant salmon. But poor river conditions force hatcheries to truck fish down to the Delta for release, Waples said. 

That’s a problem because wild salmon famously return to their natal streams to spawn. But hatchery fish, deprived of the chance to acclimate to local streams, he said, “end up pretty much everywhere.” 

“So pretty soon, instead of having multiple distinct local populations that evolved over thousands and thousands of years, you get one or a couple of really big homogenous hatchery stocks,” Waples said. “And you’ve eroded much of the genetic diversity that is really important for responding to climate change.”

Reduced genetic diversity leads to boom and bust cycles as environmental conditions in rivers and oceans change. “If there’s a mismatch, you can have a catastrophic year,” he said. “And with extinction, all you have to do is hit zero once.” 

But if you have diverse natural habitats where you let the fish fend for themselves, you’re going to get a richer portfolio of genetic adaptations, he said. “And that helps provide a buffer against big fluctuations.”

Katz and his colleagues are managing farmlands with evolution in mind. Right now the leveed river favors nonnative species like bluegill and largemouth bass that see it as the stable Mississippi they came from. They also eat endangered native fish. 

Scofield’s ill-timed expedition saddled biologists with fallacies about floodplains harming salmon for nearly a century. They’ve realized only in the past two decades that salmon evolved with seasonal marshlands. So they’re trying to figure out the best strategies to help fish recognize patterns associated with marshes while making sure they get the food they need to survive. 

One strategy might involve creating terraces along levee setbacks to give juveniles refuges from predators, as they once found in marshlands, and the same nourishment floodplains once provided. 

Toward that end, they’ve started to pump the rich mixture of invertebrates they’re growing in River Garden Farms’ fallow rice fields back into the river. “We’re in the beginning stages of this,” Katz said.

Turning Rice Fields into Fish Food Factories 

Farmers use the huge network of canals and drains in the Sacramento Valley to pull water from the river to irrigate 550,000 acres of rice, and then pump it back out to prepare the ground for planting. 

Rice farmers started flooding fields to clear postharvest stubble in the 1990s, when California restricted rice straw burning to curb unhealthy toxic emissions. Biologists quickly saw unexpected benefits. 

“Ducks and geese that had nothing to do with passing legislation suddenly looked down beneath their wings at a Central Valley that was the wetland wintering home for tens of millions of birds before it had been drained, leaving only an errant puddle here and there, and saw this vast surrogate wetlands,” Katz said, walking the land on a crisp December morning. “It didn’t take long for growers, water districts, conservationists and government agencies to recognize,” Katz interrupted himself to point out a flock of snow geese taking flight in the distance, as if on cue, casting a shimmering glow on the horizon.

“What happened,” he continued, “was this recognition that you can produce high-quality habitat on actively farmed agricultural land.”

Cornwell of River Garden Farms views the resurgence of ducks and geese on the Pacific Flyway as a generational environmental success story and a point of pride for the farming community. “Why not make salmon the next success,” he said, “and take what we learned from birds and start applying that to fish?”

One of the most important lessons? Straightjacketing the Sacramento River turned it into a food desert, so restoration must replenish the river with life derived from wetland-like habitats. Flooding rice fields during the off season mimics the way rivers once flowed across the floodplains like a liquid solar panel, letting algae and other phytoplankton soak up the energy they need to sustain a vibrant food web. 

And, as Katz and his colleagues reported in the journal PLOS ONE in September, flooded rice fields also provide energy to microbes that break down rice straw. These microbial decomposers release nutrients that complement algae to support an even greater diversity of zooplankton—water fleas, tiny crustaceans and other invertebrates—that just happen to be the perfect food for juvenile salmon. 

A growing body of research shows that flooded rice fields produce far higher densities of zooplankton, “zoop soup” as Katz calls it, than the river or canals that drain irrigated fields. In the PLOS ONE study, floodplain zooplankton densities were 53 times higher than those in the river. What’s more, juvenile Chinook raised in cages on a floodplain diet—affectionately dubbed “floodplain fatties”—grew five times faster than those raised in the nutrient-starved river. 

Last winter, the wettest on record, Katz’s team hung fish in cages on the Sacramento River near the outfall of a water district pumping station after flooding nearby fields for up to six weeks. Zooplankton density at the outfall was 40 times higher than untreated river water and caged juveniles grew 500 percent faster than those caged upstream. 

But in early December, the river ran some 30 feet below where Katz’s cages hung last year.

“If we create better habitat for fish, ducks and other critters, it’s going to free up water regulations for everybody,” said Cornwell, referring to rules that restrict water to protect endangered fish. “There’ll be more water for people, cities and farms.”

Their effort received a big boost last year, when the state budgeted more than $130 million for “multibenefit” flood projects designed to enhance public safety while supporting fish and wildlife through floodplain habitat restoration.

Back at the partially flooded field in Knights Landing, Katz pointed to what looked like a large, if perfectly straight, creek. “You could be excused if you thought that was a creek,” he said, reading my mind. “But it’s the drain, which actually is fed by more than a million acres of agricultural land on the west side of the river for this incredibly productive agricultural landscape.”

Katz plans to use that drain to pump fish food back into the water precisely when young salmon pass through. Right now he’s setting up a “Goldilocks” experiment at River Garden Farms to figure out just how long the water needs to stay on the fields to produce high-nutrient zoop soup.

The optimal recipe will give young fish enough fat reserves to weather hard times as they navigate the river on their way to the ocean. “All of that is critical to give the population the resilience to respond not just to the regular dynamic climate of California,” Katz said, “but to an increasingly severe one.”

Considering all the hurdles salmon have faced, Katz said, it’s remarkable we have any left at all. “We have really fundamentally changed the river in such a way that it doesn’t make sense to a salmon anymore. What we’re trying to do is have the system make sense to those native species.”

As Katz talked, he paused to admire a bald eagle flying above the river. Two minutes later another, then another soared high overhead like oracles delivering a message from on high: even the most imperiled species can rebound if we let them.