California’s Chinook salmon are in danger. Rice fields just might be their salvation

school of chinook salmon

Jak Wonderly

school of chinook salmon

Jak Wonderly

The Golden State's native salmon have been losing habitat to agriculture for decades. Now, they’re getting a much-needed boost from strategically flooded rice fields.

Snow geese erupt against a blue sky trimmed with fresh, white clouds. The air is so clear you can see for miles, east to the distant peaks of the Sierra Nevada and west to the gentle slopes of the Coast Ranges. But Carson Jeffres and Jacob Katz are less interested in the view above them than the one at their feet. Standing knee-deep in a flooded field at Knaggs Ranch, a rice farm near Sacramento, they peer into a floating cage made of PVC pipe and mesh and prepare to check on its unusual inhabitants.

Jeffres opens the top of the cage and dips in a small net. When he pulls it out, a pair of plump fish, each the size of a pinky finger, wriggle inside. These are young Chinook salmon—a species imperiled in California. He holds up his catch for Katz to admire.

This story originally appeared in bioGraphic, an online magazine about nature and sustainability powered by the California Academy of Sciences.

The two men are fish ecologists—Jeffres at the University of California, Davis, and Katz at the conservation-based non-profit California Trout—and they are testing a wild idea. To help save the Chinook, they are using rice fields as winter nurseries for young salmon migrating from their natal streams to the ocean.

Over the last century, water agencies have built levees along most of the state’s rivers to control floods and supply water to communities and farmers alike. But these levees also bar young Chinook from the floodplains that historically provided safe, food-rich places to grow on their journey to the Pacific. Today, more than half a million acres of these former floodplains in California’s immense interior valley are occupied by rice farms. Repurposing them as surrogate floodplains during the months they would otherwise lie fallow could be key to restoring endangered populations of wild-spawning Chinook.

Jeffres and Katz scoop salmonJak Wonderly

Carson Jeffres from the University of California, Davis and Jacob Katz from California Trout scoop a Chinook salmon fry out of a cage in a flooded rice field at Knaggs Ranch

young Chinhook salmonJak Wonderly

Carson Jeffres scoops two young Chinook salmon out of a cage in a flooded rice field near Sacramento

fish raised in rice fieldsJak Wonderly

The fish raised in the flooded rice fields at Knaggs Ranch grow quickly, thanks to a plentiful supply of freshwater crustaceans

“We can’t restore those floodplains,” says Rene Henery, California science director for the conservation non-profit Trout Unlimited, “but we can recover the functionality that the fish evolved with.”

California’s Central Valley is a flat expanse, flanked on either side by mountain ranges, that extends 400 miles down the middle of the state. Salmon once flourished in the streams and rivers that course through it. “One or two million came back every year,” says Peter Moyle, a fish ecologist at UC Davis. “They were up to 60 pounds and close to a meter long.”

For millennia, adult Chinook in California returned to spawn in the upper reaches of waterways that flow down from mountains surrounding the valley. Then, when the winter rainy season caused their natal streams to swell, the next generation of young fish would all swim downstream toward the sea, taking advantage of the many floodplains along the way.

The final stretch of their long journey would begin when the fish hit the Sacramento-San Joaquin River Delta, where the water slows, twisting and turning around the Delta’s many islands. Migrating young salmon have to navigate these braided waterways before making their way across the San Francisco Bay and through the Golden Gate Strait, the iconic narrow opening spanned by the Golden Gate Bridge that leads to the ocean.

Fish out of Water

Dams now block Chinook salmon from reaching more than 90 percent of their spawning habitat in California’s Central Valley. Additionally, water diversions and other perturbations have rendered some of their accessible habitat unusable.

Map data provided by the National Oceanic and Atmospheric Administration, January 2013.



Today, few Central Valley salmon spawn in the wild. The region’s waterways have been completely remade into a system that includes 20 major dams and more than 1,600 miles of riverbank levees. While this engineered set-up tames flooding and supplies drinking and irrigation water, these benefits to people come at a cost to salmon. Dams block entry to the mountain streams where the fish once spawned, and levees block access to the valley-floor floodplains where young salmon once found plentiful food and shelter.

Across their range, Central Valley Chinook are all classified as a single species, but for management purposes the fish are divided into four runs according to the season when adults return from the Pacific Ocean to spawn. Two of those runs are listed under the federal Endangered Species Act, while the other two are considered federal populations of concern.

Engineered rivers are almost completely to blame. “Just as we’ve lost almost all the floodplain habitat, we’ve also lost pretty much all of the spawning habitat,” says Brian Ellrot, the Central Valley salmon recovery coordinator at the National Oceanic and Atmospheric Administration (NOAA), which leads the efforts to restore populations of these fish.

Canal and irrigation systemJak Wonderly

An aerial view of a canal and irrigation system near the Sacramento River illustrates how heavily engineered the landscape has become

“They’re just straggling along right now,” Jeffres says. “They’re propped up by hatcheries.” State hatcheries release more than 32 million young salmon annually, and these fish dominate all four runs of Central Valley Chinook.

The best way to restore Chinook salmon, fish biologists say, is to give them back some of what they’ve lost. To provide more spawning grounds, NOAA plans to start transporting migrating adults past Central Valley dams―from the downstream side to the upstream reaches―as is done by wildlife agencies in the states of Washington and Oregon.

Restoration of degraded spawning grounds below dams will also be critical to their recovery. While most salmon return to their natal waters to spawn, a few stray in search of new homes. This penchant for exploration allows them to revisit waterways where they had previously been extinct for decades. Recent restoration efforts are starting to pay off: After an absence of 70 years, Chinook now return by the hundreds to spawn in Putah Creek, a tributary of the Sacramento River. Likewise, for the first time in more than half a century, a couple dozen Chinook have found their way back to historical spawning grounds in the San Joaquin River, which flows from the Sierra Nevada to the Delta.

dense flock of snow geeseJak Wonderly

A dense flock of snow geese lifts off from a flooded rice field in California’s Central Valley

Restoring floodplain nurseries is a harder problem to solve, since this habitat has been more dramatically altered and requires changes on a much larger scale. Repurposing rice fields in the off-season may be a big part of the answer, and NOAA is supportive of the effort. “We’re pushing to make that happen,” Ellrot says. “Salmon are really resilient―I’m optimistic that if we give them the right nudge, we can restore them in the valley.”

Restorationists have good reason to think that prime nursery grounds are vital to the long-term survival of the region’s salmon. The most robust population of spring-run Chinook originates in Butte Creek, which runs along a wildlife refuge that contains some of the valley’s few remaining floodplains. The Butte Creek salmon population is wild-spawning and self-sustaining. “It’s the one successful population of spring-run salmon,” Jeffres says. Young salmon here are more likely to make it out to sea, and the adults more likely to return and spawn.

“Fish abundance equals water security. It doesn’t have to be fish versus farms―it can be fish and farms.”

A probable reason for Butte Creek’s success is that it gives Chinook a place to grow and thrive. The creek’s young fish are larger than those elsewhere in the valley, and being bigger presumably boosts survival. “It makes the salmon more resilient,” Katz says, just like packing lunch before a long trip.

restored wetlandsJak Wonderly

An aerial view of restored wetlands in the Sacramento River floodplains near Knaggs Ranch

Before scientists understood the value of floodplains, they considered them risky for fish. “Wildlife biologists thought floodplains were bad for salmon because they stranded them, and that levees were good for salmon because they kept them in the river,” Moyle says. “It was pretty much unquestioned.”

It’s only in the last two decades that this conventional wisdom has been overturned. The first evidence came from scientists looking at the fate of young salmon in the Yolo Bypass. Built to contain a floodplain of the Sacramento River, the Bypass is an enormous flood control structure—about 40 miles long and two miles wide—that shunts water from the Sacramento River around the City of Sacramento. It’s bounded on either side by colossal, earthen levees that are more than 20 feet high and wide enough to drive on. When the river runs high, it overtops a weir at the north end of the levees. Water spills down inside the bypass, flooding it, then rejoins the river at the south end of the levees.

The Yolo Bypass only fills during the winter, and, when it does, some of the young salmon migrating downstream come along for the ride. During particularly wet winters, the bypass is so full it looks like an inland sea. “The floodplains are still there,” Katz says. “They’re just used differently, as bypasses.” A 1998 study concluded that salmon swept into the bypass grew faster than those that remained in the river.

Jeffres got similar results when he looked at fish in the Cosumnes, one of the state’s rare, free-flowing rivers that still has remnants of natural floodplains. In 2004, he found that young salmon in a floodplain grew faster than those in the Cosumnes River itself.

Katz examines water sample Jak Wonderly

Jacob Katz examines a water sample full of zooplankton, pulled from a flooded rice field at Knaggs Ranch near the Sacramento River

In 2009, the California Department of Water Resources decided to give salmon about 20,000 acres of floodplain habitat―one-third of the total acreage―in the Yolo Bypass. Most of the land there is privately owned and farmed for rice during the summer growing season. That decision caught the attention of rice farmer John Brennan, who wanted to keep fields in production in the Yolo Bypass.

Water is in short supply during the hot, dry Central Valley summers, especially during the state’s periodic severe droughts. Historically, the fight over this constrained resource has pitted growers against environmental laws that require allocating water for endangered fish like Chinook. Rather than playing this zero-sum game, Brennan has been looking for ways to integrate conservation with agriculture. “If you’re in the rice business, you’re in the water business―and if you’re in the water business, you’re in the fish business,” he says.

Katz puts it this way: “Fish abundance equals water security. It doesn’t have to be fish versus farms―it can be fish and farms.”

In flooded rice fields like this onenear the Sacramento River, the shallow, still water provides the perfect conditions for both algae and zooplankton to proliferate

Chinook salmon in handJak Wonderly

Jennifer Kronkfrom California Trout prepares to weigh and measure a young Chinook salmon

measuring salmonJak Wonderly

Jennifer Kronk records fish measurements and tagging information at a sampling site

In 2010, Brennan joined forces with two environmentalists to see if rice fields in the bypass could be used as salmon nurseries during the winter, when the fields are dormant and fish are migrating downstream. After scouting the Yolo Bypass for available properties, Brennan and his partners settled on the rice fields of Knaggs Ranch as a chance to put their plan into practice. They bought the ranch and assembled a research team, starting with Jacob Katz since his father is one of Brennan’s partners. Katz invited Jeffres to join him, and the pair has collaborated ever since.

In the winter of 2012, the researchers flooded a five-acre corner of the ranch and released 10,000 young hatchery salmon in the fallow field. “When we first started, lots of farmers laughed and said it was the stupidest thing they’d ever heard,'” Jeffres says. He and Katz had their doubts, too. “It didn’t look like fish habitat,” Jeffres says, pointing across the ranch to their original test site. Flat brown fields stretch in all directions, and tidy mud berms divide the land into a patchwork of close-packed rice paddies. “We thought it might be the dumbest thing we’d ever done.”

Chinook salmon measuredJak Wonderly

A Chinook salmon fry is measured at the Bodega Marine Laboratory at the University of California, Davis

They worried they’d end up with a field full of dead fish. They weren’t concerned about residual pesticides, which are applied months earlier and break down relatively quickly in the environment, but they fretted about a host of other potential pitfalls. They thought the stagnant, shallow water in the field might get too warm for fish or make them easy prey for hungry birds. And they didn’t know whether the decomposition of rice stubble, which is left on the fields after the fall harvest, would deplete oxygen levels in the water.

At first the researchers couldn’t tell whether anything was happening. “Out in the fields in mid-winter it looks like a mud puddle. We couldn’t see the fish,” Katz says. “Then we ran a net through the water and caught fish with little potbellies. It was amazing.”

Their rice-field test subjects did far more than survive. They thrived, growing five-fold―from 1 gram to more than 5―in just six weeks. “They grew at the highest rates recorded in the Central Valley,” Jeffres says.

Ultimately, the scientists envision that the young salmon, instead of being introduced into rice fields by humans, will leave their natal waters and migrate downstream and into the bypass on their own. To make that journey possible even if the weir hasn’t overflowed, the California Department of Water Resources wants to add gates that can be opened to let salmon swim in and out of the rice fields on their way to the ocean.

While there are still some barriers left to remove, the possibility of wild-spawning, self-sustaining Chinook runs raised on rice farms is no longer just a pipe dream. In the years since they launched their pilot project, Jeffres and Katz have expanded their effort to encompass 20 acres and 50,000 fish, proving that it can work on a real-world scale. They have also found that, on average, salmon reared in these rice-field nurseries weigh 12 times more than those that grow up in the Sacramento River. The reason for this, Jeffres says, is that there’s so much more for them to eat.

water sample from rice fieldJak Wonderly

This water sample, taken from a flooded rice field near the Sacramento River, is thick with small freshwater crustaceans in the genus Daphnia. The crustaceans are a nutritious food source for young salmon

Back at Knaggs Ranch, Jeffres wants to know just how much more food the rice fields contain. He casts a long, white net across the shallow water of a rice field then draws it back carefully, keeping clear of the mud. Katz tips the contents into a plastic bag and lifts it high so they can both see.

“Holy shit! Holy shit! Holy moly!” Katz exclaims. “I am totally astonished.”

Jeffres is equally jazzed. “That’s insane!”

Inside the plastic bag, tiny freshwater crustaceans―or “bugs,” as the researchers call them―dart back and forth in constant motion. The water is so thick with them that it looks like a whirling cloud of pink.

These small crustaceans are the perfect food for young fish, and this haul is the best Katz and Jeffres have ever seen. Most of the bugs they netted belong to the genus Daphnia, often dubbed water fleas for the way they swim in short hops. They’re here in such abundance because they thrive in shallow, algae-rich waters, from puddles to flooded fields to floodplains. “It’s magic when water slows down and spreads across a floodplain,” Katz says. “It’s liquid protein.”

Pickings are far slimmer in rivers. Katz holds up another bag, this one netted about an hour earlier from the Sacramento River. Just a few crustaceans scoot around inside it. “There’s basically nothing here,” he says. “By building levees, we’ve created rivers that are essentially food deserts.”

Katz throws a siphonJak Wonderly

Jacob Katz throwsa siphon to collect a water sample in a flooded rice field near the Sacramento River

The Sacramento River has several flood control bypasses, and Katz estimates that, altogether, they contain up to 150,000 acres of rice fields that could be used as bug-rich salmon nurseries. Another 500,000 acres of rice farms lie along the Sacramento River but outside bypasses―and he thinks they may be able to help salmon, too.

One of these is River Garden Farms, which lies a short stretch upriver from Knaggs Ranch and is managed by Roger Cornwell. Like Brennan, Cornwell wondered if his fields could benefit salmon, despite the fact that the land is not in a bypass. “I met Jacob Katz and started talking to him about what we could do,” he says. Katz proposed another wild idea, one that could solve the food-desert problem: bug farming.

They wanted to know, Jeffres says, “If we can’t bring the fish to the floodplain, can we bring the floodplain to the fish?”

Katz examines contents of siphonJak Wonderly

Jacob Katz examines the contents of asiphon after collecting a water sample in a flooded rice field near the Sacramento River

River Garden Farms is separated from the Sacramento River by a levee, atop which sits the Rough and Ready Pumping Plant, which was installed in 1915 to irrigate fields. The plant houses five glossy, black, massive pumps—each about six feet tall—which fill the pump house with a low roar. This past winter, the team took advantage of the setup and flooded a fallow rice field to raise bugs, then pumped the food-rich water into the Sacramento River to feed young fish as they swam through.

To test whether the bugs would reach their intended recipients, the researchers placed cages of young salmon at intervals along a mile or so of the river. The Rough and Ready pumps delivered bugs starting in late February, and Jacob Montgomery and Jennifer Kronk of California Trout took weekly measurements of the caged fish. By late March, when we visit, all the bugs have been pumped off the field. The field crew pulls on their waders and heads out to the river to see if the experiment worked.

Kronk rinses siphonJak Wonderly

Jennifer Kronk from California Trout rinses the contents of a siphon into a specimen bag in order to measure the amount of zooplankton present

They start at a site upstream of the pumping plant, where the caged fish didn’t get any field-raised bugs. Montgomery and Kronk wrestle a cage to the river’s muddy bank. Montgomery hefts the cage above the water, revealing young salmon that flash silver as they flip back and forth in distress. The team works fast so as to get the fish back to the river as soon as possible. Montgomery places each fish in a tray with a ruler, splashing it with water to keep it calm and still, and calls out the length for Kronk to record. Then he passes it to her for weighing. When the measuring is done, he estimates that the upstream fish averaged about 55 millimeters long and weighed around 2 grams.

Moving downstream to the next site, Kronk scoops up a fish collected right by the pump outfall. This site got the most bugs delivered from the rice field―if the experiment works, they’ll see it here.

“Oh, he’s fat,” Kronk says.

water samplesJak Wonderly

On the left, a water sampletaken from a flooded rice field is bursting with zooplankton. On the right, a water sample taken from the Sacramento River on the same day contains very little food for young salmon

She lays it in the measuring tray. It’s 65 millimeters and 2.5 grams, considerably bigger than the upstream average. The next fish is even fatter, at 66 mm and just over 3 g, and the one after that is fatter still, at 71 mm and 4 g.

“Wow, look at these guys. They’re doing great,” Montgomery says.

Although supplying bugs to fish in a free-flowing river doesn’t guarantee delivery, a system that monitors migrating salmon is already in place―so the researchers will know when to expect the fish and can serve them food from the fields at just the right time. “We can pump bugs into the river when fish are passing by,” Katz says. By spring, the salmon will have completed their journey, and the rice fields will be drained and ready for planting.



Fish biologists have long assumed that the larger young salmon are when they navigate the Delta, the faster they can swim and the better their chances of survival. “It’s a really dangerous place,” Trout Unlimited’s Rene Henery says. “There are lots of introduced predatory fish.” To date, however, there is no direct evidence that size is important to survival.

“In the fish world, we say bigger fish are more likely to make it to the ocean. But no one has actually looked at survival,” says Rachelle Tallman, a graduate student in fish ecology at UC Davis. Tallman is now heading up a project to do just that.

The project is part of an effort by the California Rice Commission to incentivize farmers to manage their rice fields in a way that benefits local wildlife. Paul Buttner, who manages environmental affairs for the commission, currently pays farmers to flood their fields for water birds migrating along the Pacific Flyway. He hopes to launch a similar program for salmon that would compensate farmers for creating floodplain nurseries for young, migrating fish. But first he needs solid proof that it works.

“How many salmon from fields survive and go out the Golden Gate?” Buttner asks. “More than those that grow up in the river?”

While the Rough and Ready plant was pumping bugs into the Sacramento River, Tallman was setting up a different experiment to assess how size affects a salmon’s success. She reared two sets of young salmon: some in a laboratory tank and others in rice fields in the Yolo Bypass. Now, on a warm April day near the edge of the bypass, she’s pulling fish from the rice fields and equipping them with acoustic tags so she can compare survival rates as they swim out to, and beyond, the Golden Gate.

Davis grad student inserts tracking tagJak Wonderly

Rachelle Tallman, a graduate student at the University of California, Davis, makes an incision in the abdomen of a salmon fry to insert a tracking tag

Tallman stands at a fish-surgery station sheltered by a white tent. As she slips a young salmon into a bucket of anesthetic, she alerts her team that a surgery is in progress. “Dope!” she calls out.  A minute later the fish has stopped wriggling and Tallman springs into action. In rapid succession, she weighs it, measures it, and places it on a foam block. Cool water streams across the fish, which lies motionless apart from flapping gills.

Surgical scissors in hand, Tallman cuts a small opening in its belly and pushes a centimeter-long tag inside. She closes the wound with a single stitch and knots both ends. “Fish out of surgery,” she calls. A crew member collects the salmon and puts it in a recovery bucket. The whole operation, including anesthesia, takes just two minutes. Then Tallman picks up another fish and starts the process anew. “Dope!” she says.


Back at the lab, another crew tags tank-reared fish. Collectively, the team tags more than 750 salmon.

A day after the surgeries, Tallman releases her tagged salmon into the wild, sending some into the Sacramento River and some into the Yolo Bypass, which drains into the Sacramento. About 200 underwater acoustic receivers will track their progress.

By early May, the first tagged fish have navigated the perils of the Delta. Now, they must traverse the San Francisco Bay—a huge body of water that covers more than 500 square miles. But this part of their journey is less risky. Once they’ve gotten this far, most young salmon readily find their way across the Bay and swim through its narrow opening beneath the Golden Gate Bridge, out into the Pacific Ocean. It will likely be December before Tallman can crunch all the data and tell Buttner whether—and how much—the rice field nurseries boost survival rates for the salmon. While the final verdict is still out, Buttner says they’re all hoping for a nice Christmas present.

The fish in Tallman’s study that do make it to the Pacific and survive in the open ocean will eventually attempt to return as adults to spawn in the Central Valley’s extensive but highly altered river system. It’s a journey the scientists hope will become at least slightly less challenging in the years to come. “We’re not going to get back what we once had,” Jeffres says. “But we can mimic it.” He and Katz envision waterways that are managed for flood control and farming but also for Chinook survival, ones with rice-field nurseries and bug farms to help restore self-sustaining salmon populations.

“It’s about welcoming the wild back into human landscapes in a way that makes sense,” Katz says. “We’re reimagining the system to work with nature.”

This story originally appeared in bioGraphic, an online magazine about nature and sustainability powered by the California Academy of Sciences.

Robin Meadows is a science journalist in the San Francisco Bay Area. Recent stories have taken her to former commercial salt ponds in the San Francisco Bay, homeless encampments along creeks, and a Superfund Site on tribal land. She is the water reporter for the Bay Area Monitor, and her work has also appeared in Audubon, Conservation, High Country News, Nature, and others.

Jak Wonderly has had stories published in National Geographic, Sunset, the Los Angeles Times, Wine Spectator, American Cowboy, Alaska Airlines magazine, and CNN among others. Commercially, he photographs agriculture, travel, and equestrian subjects. He is represented by National Geographic Image Collection. Wonderly has worked on assignment for The Nature Conservancy, Wild Wonders of China, and the Snow Leopard Conservancy, and volunteers at his local wildlife rescue in Sonoma County, California.