In 2012 a team of salmon researchers tried a wild idea: putting pinky-sized Chinook on a rice field in the Yolo Bypass, a vast engineered floodplain designed to protect the city of Sacramento from inundation. The team found that rearing fish on farms works better than they had ever dreamed. Salmon in this managed floodplain grew so fast — averaging more than one millimeter per day — that they outpaced young Chinook elsewhere in the region. Now, after nearly a decade of testing fish in fields, a new paper in San Francisco Estuary and Watershed Science outlines lessons learned as well as next steps in managing floodplains for salmon.

“There’s some urgency,” says lead author Ted Sommer, a native fish expert at the state Department of Water Resources, which manages the Yolo Bypass as a floodway. “There’s been a long-term decline in Chinook salmon.”

Floodplains once served as nurseries for young salmon migrating from mountain streams to the ocean. Today, however, most of the low-lying land along California rivers is leveed and farmed. “They’re one of the more important areas we could improve,” Sommer says. “We’re looking for creative solutions — can we make farming more fish friendly?” The big question is whether fields that produce rice can also be managed as floodplains.

Basin to bypass

The Yolo Basin was once an enormous wetland along the Sacramento River, covering an area about 40 miles long and up to seven miles wide from what is now Knights Landing to the Sacramento-San Joaquin Delta. Early accounts described the basin as an immense sea during severe winters. As rainstorms swelled the river and local streams, floodwaters overtopped their banks and spread over the basin at depths ranging from as much as 20 feet by the riverbanks to just a few inches farther out. These floodwaters moved slowly in a broad sheet through the wetlands to the Delta, taking so long to drain that the basin was impassable half the year.

Riparian forests thick with cottonwoods, sycamores, and oaks grew on natural streamside berms. The rest of the Yolo Basin was dominated by freshwater marsh filled with dense stands of tule more than 10 feet high. In an 1870 volume called The Western Shore Gazetteer, Yolo County, C.P. Sprague and H.W. Atwell told of “simply immense rushes, which cover the ground with an almost impenetrable thicket.”

Herds of tule elk wandered the basin’s marshes and grizzly bears abounded. Astonishing numbers of geese and ducks thronged to the basin to feed and rest during their winter migrations along the Pacific Flyway. Lansford W. Hastings recounted the spectacle in his 1945 book The Emigrants’ Guide to Oregon and California, describing the innumerable flocks as “at times blackening the very heavens,” and their “tumultuous croaking and vehement [squawking]” as almost deafening.

The Yolo Basin was also a paradise for salmon and other fish. Young salmon grew big and fat in the basin’s floodplain nurseries on their way down to the ocean, and returning adults swam back up the basin toward their natal spawning grounds. Salmon were so plentiful that people with handheld nets hauled in tremendous catches from the banks of the Tule Canal, an early effort to drain the basin that was built in 1864.

Today much of this historical floodplain is occupied by the 59,000-acre Yolo Bypass. Built about 100 years ago, the bypass is an imposing structure: 40 miles long, two to three miles wide, and bounded by 20-foot earthen levees. Sacramento River floodwaters pour into the bypass at the top and flow out to the Delta at the bottom. The land in the bypass is a mix of private farms and duck clubs and public wildlife areas. 

Managed floodplains

Given these extensive alterations, it’s no surprise that biologists assumed the Yolo Bypass was no longer a good place for fish. That perception began to turn around in the late 1990s, when Sommer went into the bypass and saw that many fish species thrive there in wetter winters. “We found that it was a major fish nursery,” he recalls. In hindsight, it makes perfect sense because even now the bypass is an expanse of inland sea after heavy rains. That said, it was still a big leap to put young salmon on rice fields. Even Sommer had doubts.

He knew pesticides wouldn’t be a problem in winter-flooded rice fields. These agricultural chemicals are applied in the spring and break down fast in the environment. But he did worry that decomposing rice stubble, which is left on the fields after the fall harvest, would use up oxygen in the water and suffocate the fish. “I was nervous initially — but despite the fact that we’re taking about agricultural fields, it’s pretty good fish habitat.”

Young salmon flourish in winter-flooded rice fields because these managed floodplains are spectacularly rich in tiny crustaceans, informally called “bugs,” that make terrific food for little fish. “This is one of the key cool findings,” Sommer says. The team learned that building up this abundance of food takes about three weeks. “It’s not enough to get the floodplain wet, you have to keep it wet so bugs can grow and the fish can get big,” says Jacob Katz, a fish ecologist at California Trout who is a co-author of the paper. “That’s the key to survival once they reach the ocean.”

The problem is that the bypass is engineered to drain rapidly. While the land there is inundated when it rains a lot, it drains in a matter of days in drier winters. And that, Katz explains, is when managed floodplains can do the most for young salmon. “The bypass is already a good place to be a fish during wet years,” he says. “The challenge is that during dry years, there’s very little floodplain habitat.”

Managed rice fields could create salmon nurseries in the bypass even when rain is scarce. “Passive restoration is not enough,” Katz says. “We can use infrastructure to mimic historical floodplains.” He envisions augmenting berms to hold floodwater in fields longer and installing operable gates to drain the fields and release fish.

Dos and don’ts

Actively managing fish on fields requires some finesse, however, as the team learned at the height of the 2012-2016 drought. Their experimental flooded rice field was one of the only wetlands for miles around, drawing cormorants, egrets, and great blue herons that picked off the young salmon. “California’s seesaw climate is a challenge for managed wetlands,” Sommer says. “I wouldn’t recommend them during a historical drought.”

Carson Jeffres, an ecologist at the UC Davis Center for Watershed Sciences and another co-author of the paper, chalks this instance of high bird predation up to experience, explaining that we need to understand what works and what doesn’t to inform management actions. The lesson he draws is that “if you have the only spot out there, that’s not good — but a mosaic of floodplain habitats could work.” Boosting the number of flooded fields would give waterbirds more places to hunt, which could lessen the risk of creating predation hotspots.

The team also identified the primary factors critical to the success of managed floodplains. “Flow and connectivity are essential,” Sommer says. “Fish are consistently attracted to inflows and outflows so they can’t be in a pond — you have to keep flow through the field.” In addition, when salmon leave the field, they need a reliable connection to natural habitat so they don’t get stuck or eaten. “You need a clear exit corridor that drains well so fish can move out quickly and freely.” Getting young salmon off fields safely will require nimble hands-on management.

The goal is to balance keeping fish on fields long enough to maximize the floodplain benefits with releasing fish while there’s still enough water to make it to the Delta. That timing can vary widely depending on the weather, from as early as mid-February in a dry year to as late as early June in a wet year. “Ecosystems are not bound by dates on the calendar,” Jeffres says. “You need to look at the system as a whole, track the forecast, and time the migration to conditions.” He proposes a salmon czar to oversee and coordinate these logistics, comparing this to the role waterkeepers play for rivers and streams.

Wild fish 

So far, all the team’s test salmon have been trucked in from hatcheries and poured directly onto flooded fields. Co-author Bjarni Serup would like assurances that wild fish will also benefit from managed floodplains before implementing  them on a large scale to the Yolo Bypass. “We’d like to see whether we can get natural-origin fish on and off fields,” says Serup, an environmental scientist at the California Department of Fish and Wildlife. Questions include whether wild salmon will swim to rice fields on their own when the bypass floods, and whether growing up in fields increases their odds of survival to the ocean.

Projects that could help provide answers are underway. A joint California Rice Commission-UC Davis study is fitting field-reared salmon with acoustic tags and tracking their survival after release. Moreover, DWR is installing a 100-foot-wide notch in the Fremont Weir, a two-mile-wide concrete wall at the top of the Yolo Bypass that controls when floodwaters spill in from the Sacramento River. Currently, this happens during big storms and the retrofit will also allow water over the weir during smaller storms. This will flood the bypass more often and could also make it easier for young wild salmon to swim into the bypass and onto managed floodplains. Construction of the $190 million Fremont Weir notch project is scheduled to begin in 2022.

Another unknown is how to design managed floodplains that work for both young and adult salmon on the Yolo Bypass. “It’s like a highway with traffic in two directions,” Serup says. “Young fish are swimming downstream and adults are swimming upstream so there’s potential for conflict in rice fields — water control structures are just not good for adult fish.” Agencies are working to minimize obstacles for migrating adult salmon in the bypass. “They’re high-value individuals,” Serup says. “They’ve returned to spawn.”

Scaling up

John Brennan, who owns the Yolo Bypass rice farm that hosted most of the team’s work over the last decade, is more than ready to move forward on managed floodplains. “The weirs are getting notches, and there’s side channel and gravel bed restoration along the Sacramento River from Shasta Dam to Chico,” he says. “What’s missing is floodplains.”

Brennan is all set to create expansive managed floodplains. One reason the bypass drains so speedily is that it slopes five or six feet from the top to the bottom. Brennan proposes building four-foot berms on the low side of farmed lands to keep water from sheeting off, and inundating thousands of acres in the bypass for salmon nurseries. He’d love to see these managed floodplains folded into the Fremont Weir notch project.

“It’s going to be fantastic when it all comes together,” Brennan says. “The ultimate dream is to ramp down the hatcheries and have wild fish take over.”

Look for this new paper in San Francisco Estuary & Watershed Science this fall.

Related Estuary News Stories

Network Listens for Passing Salmon, March 2020

Boosting Chinook, December 2019 

Clout and Cool Science Push Land-River Reconnection, September 2019

Putah Creek Pipeline for Salmon, March 2019 

Simple Isn’t the Answer for Salmon, September 2019 

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Top photo: California Trout’s Jacob Katz and Jennifer Kronk walk to sampling site in the Yolo Bypass. Photo: Jak Wonderly