By Robin Meadows
A new strategy could help California water managers meet the needs of people as well as the environment. This could benefit at-risk species like shorebirds and salmon that historically flourished in the state’s great Central Valley, which stretches 450 miles from Redding to Bakersfield. Today people use so much water in this intensively farmed region that rivers can run dry.
The strategy arose from a pilot analysis—called the Merced River Basin Flood-MAR (Managed Aquifer Recharge) Reconnaissance Study—that modeled using flood flows to recharge groundwater in the Merced River watershed. The goal was to optimize aquifer storage, reservoir storage, and environmental flows.
“We think it’s a new, better way to integrate these three sectors and get them working together,” says Technical Studies Manager David Arrate, a water resources engineer with the state Department of Water Resources who presented this work during a July 2023 workshop. “It could provide benefits to the water supply and ecosystems.” The Merced River Basin study is wrapping up, with final reports expected soon, and next the team will expand their analysis to the San Joaquin River Basin.
Looking at the Central Valley today, it’s hard to believe that roughly a century ago this agriculture-dominated expanse had vast wetlands bursting with wildlife. The land is so flat that during the wet season, rivers overtopped their banks and spread tens of miles, inundating more than four million acres or nearly one-third of the valley floor.
Millions upon millions of waterbirds rested and refueled in these ephemeral waters while migrating along the Pacific Flyway, which connects Alaska with South America. Chinook salmon runs were among the largest on the Pacific Coast, with as many as two million adults returning to spawn each year, and throngs of their young grew fat in river floodplains on their way toward the sea.
Today California’s shorebirds and salmon are in trouble, and the wetland stopovers that these species rely on are scarce and much altered. People drained more than 90 percent of Central Valley wetlands, and built flood-control levees that disconnected rivers from 95 percent of their floodplains.
Habitat restoration for Central Valley waterbirds and salmon is underway. But the success of these efforts depends on having water to inundate the land when and where these species need it. The Merced River Basin study points to a way to do just that.
MULTIBENEFIT MANAGED AQUIFER RECHARGE
The Merced River runs 145 miles—from 13,000-foot high headwaters in the Sierra Nevada to its confluence with the San Joaquin River about 85 miles south of Sacramento—and drains nearly 1,300 square miles.
The system’s main reservoir, Lake McClure, is in the Sierra Nevada foothills and holds up to one million acre‐feet of water, enough for up to two million households or nearly 300,000 acres of farmland. Dams, channel simplification, and levees have all but eliminated floodplain inundation along the Merced River downstream of Lake McClure.
The idea behind the Merced River Basin study was to roll multiple benefits into managed aquifer recharge at a watershed scale. Arrate and colleagues modeled the impact of combining two emerging approaches to water management in the Merced River watershed. The first approach is managed aquifer recharge, which entails diverting high flows from rivers to land such as orchards, crop fields and floodplains. Once there, the water percolates through the soil and replenishes groundwater basins.
The second approach entails managing reservoirs according to forecasts for atmospheric river storms, which have become more accurate in recent years. This approach is called forecast-informed reservoir operation, or reservoir reoperation for short.
Many California reservoirs also serve as flood control basins, and water releases are mandated to help prevent flooding during the winter. Currently, however, these releases are made based on historical weather patterns rather than whether or not a big storm is actually coming. Under reservoir reoperation, water levels could be kept higher safely when the forecast shows there’s no storm in sight.
“If the five-day forecast is showing no storm, can we save more water at a rate that meets all downstream demands, move more water into the ground for recharge, and bank some water for eco-actions?” Arrate asks. Eco-actions include inundating wetlands and other floodplain habitats when shorebirds and young salmon are migrating.
The Merced River Basin study suggests the answer to Arrate’s question is yes.
WATER FOR WILDLIFE
To predict how implementing first managed aquifer recharge and then reservoir reoperation could affect future storage in Lake McClure, the team simulated a century of hydrology (1900 to 1999) under 30 climate change scenarios (a temperature increase ranging from 0° to 4° C, and a precipitation change ranging from 20 percent less to 30 percent more).
Adding reservoir reoperation to managed aquifer recharge is key. “That’s when you really see all these benefits,” Arrate says. Notably, reservoir reoperation could allow banking more water in Lake McClure. This water could then be released for migrating shorebirds and young salmon.
Taylor Spaulding, a biologist at the environmental consulting firm ESA Environmental, evaluated the potential for these ecosystem benefits at the 2022 International Symposium on Managed Aquifer Recharge. Specifics for wetland habitat were based partly on criteria from the California Environmental Flows Framework, which is developing guidelines for managing rivers more naturally, and The Nature Conservancy (TNC), which pays farmers and private wetland managers to provide habitat for Central Valley waterbirds via its BirdReturns program.
Spaulding estimates that shorebirds could gain 521 acres inundated to a depth of at least two inches during March. Likewise, young salmon would gain floodplains inundated to a depth of one foot for at least two weeks during April or May. Noting that floodplains are “very limited” in the Merced River, he says reservoir reoperation could create a “marked increase” in salmon rearing habitat.
RESTORING WETLANDS FOR SHOREBIRDS
Julia Barfield, Program Manager for TNC’s BirdReturns, is excited at the prospect of more wetlands for shorebirds. “It’s tremendous that the Department of Water Resources is thinking holistically about water and considering the needs of wildlife,” she says.
Flooded habitat on Central Valley farmland and managed wetlands, such as duck clubs, supports some seven million waterfowl and 350,000 shorebirds each year, according to Audubon California. While many waterbirds are rebounding, shorebirds have declined 40 percent in the last 50 years. “It’s pretty severe,” Barfield says. “They have an extreme habitat shortfall.”
Shorebirds, which migrate up the Pacific Flyway in the spring and back down in the fall, have very particular requirements. Central Valley wetlands are often flooded to depths of a foot or more, which suits waterfowl like ducks.
But shorebirds need much shallower wetlands so they can get to the mud-dwelling invertebrates they eat. “They walk on the surface of the mud and probe it with their bills,” Barfield says. The shorter the birds’ legs, the shallower the water must be.
While long-legged species like the black-necked stilt can feed in water four inches deep, “Least sandpipers have really tiny legs so they need it really shallow,” Barfield continues. “One to two inches is ideal.”
RESTORING FLOODPLAINS FOR YOUNG SALMON
Alison Whipple, a hydroecologist at the San Francisco Estuary Institute, says scenarios of future water supplies like that laid out by Arrate and his colleagues in the Merced Basin Study could inform current floodplain restorations for young salmon in the Sacramento Valley.
“We’re using flow data from the last 20 years but with climate change, those flows might be different,” she says. “It would be really valuable to look at possible scenarios for future flows—we could plan restorations to take advantage of those.”
Young salmon need water that is relatively shallow and slow. Reconnecting rivers with their former floodplains typically involves breaching levees, and Whipple’s expertise includes predicting how water will spread over a landscape afterwards as well as and how that will benefit a given ecosystem.
To help assess various options for floodplain restoration, she was part of a multiagency collaboration that developed the Chinook Salmon Habitat Quantification Tool. “It uses hydrodynamic modeling results to evaluate the extent, depth and velocity of inundation over space and time,” Whipple says. Then the tool “ranks salmon rearing habitat from good to bad and determines where and what type of restoration, or what flow conditions, might have the greatest benefit.”
Whipple is part of a team applying the Chinook Salmon Habitat Quantification Tool’s approach in an initiative called Floodplains Reimagined, which launched in 2021 and aims to reconnect floodplains for salmon and birds in ways that are compatible with agriculture in the Sacramento Valley’s Butte, Colusa and Sutter basins.
“If we can work out where the opportunities are and which actions have the greatest potential, there’s more we can do to maximize floodplain rearing habitat for salmon while meeting multiple objectives in our highly modified landscapes today,” she says. “It’s a big, ambitious project.” The new water management strategy outlined by Arrate and colleagues could help tip such habitat restorations for Central Valley wildlife toward success.
