by Robin Meadows
In 2021, California suffered a severe drought and the hottest summer then on record. Water was beyond scarce. It was brutal for the fish, farmers and others who depend on flows in the San Francisco Bay-Delta watershed, a system that spans hundreds of miles from mountain headwaters to the confluence of California’s two longest rivers, the Sacramento and the San Joaquin.
But that year also saw the beginnings of a new National Academies study to help California’s imperiled salmon, smelt and sturgeon survive people’s relentless water diversions from the Bay-Delta system.
Supplying water without sacrificing fish is a “massive, high stakes balancing act,” says Dave Owen, a UC Law, San Francisco professor who has a background in geology and focuses on water resource management. “Science helps strike that balance.”
Two colossal water projects divert flows to millions of acres of farmland and nearly 30 million Californians. One is the 400-mile long Central Valley Project, which is run by the Bureau of Reclamation; the other is the 700-mile-long State Water Project, which is run by the California Department of Water Resources.
The new National Academies study, which came at the request of the U.S. Bureau of Reclamation, is the first in a biennial series reviewing the scientific underpinnings of key water project actions in the Bay-Delta system. After signing the contract with the Bureau of Reclamation in the summer of 2023, the National Academies convened a committee of 18 experts to undertake the study. Next came two years of meetings, field trips, and deep dives into the underlying science. The study culminated late last year with a 352-page report detailing the committee’s findings and recommendations.
To learn more, Maven’s Notebook asked six committee members with a range of expertise for their takes on what’s new and/r notable in the report.
THE SCIENCE IS SOUND
Committee member Owen points out that what’s not in the report is just as important as what is. “You won’t see a scathing indictment of the way science in the system is being done,” he says. “We found no lack of integrity in the science, just a lot of challenges.”
For help meeting these challenges, the Bureau of Reclamation asked the committee to zoom in on three specific water project actions: managing cold water in Lake Shasta to boost the survival of winter-run chinook eggs in the summer, managing the Old and Middle river flows that pull fish toward the Delta pumps, and making parts of the Delta more hospitable to young Delta smelt in the summer and fall.
SHASTA COLD WATER POOL
Winter-run chinook once laid their eggs in great abundance in the McCloud River system on the slopes of Mount Shasta, where glacier-fed springs keep the water cold even during the heat of the salmon’s summer spawning season. Today Shasta Dam blocks access to their historical spawning grounds. Instead, the fish make do with a stretch of Sacramento River near Redding, where summers are so hot that their eggs and hatchlings often perish. To help these very early life stages of winter-run chinook, the Bureau of Reclamation saves a pool of cold water in Shasta Lake for release during the summer.
This action is unlikely to be enough in the long term as the world warms. “Winter-run chinook are vulnerable to over three years of consecutive drought,” says committee member Steven Sadro, a UC Davis limnologist. “It’s a no-brainer―we know it’s going to happen, it’s not a question of if but when.”
Rather, the future of winter-run chinook depends on ongoing restoration efforts in their historical spawning grounds in Battle Creek and the McCloud River. The latter is a government agency collaboration with the Winnemem Wintu Tribe, whose traditional homelands flank the McCloud and whose lives are entwined with those of the salmon.
In the meantime, however, the Shasta cold water pool is essential to saving winter-run chinook. The committee’s recommendations include additional temperature sensors in the reservoir and river system, which would provide more accurate estimates of the availability of cold water.
But warm water is far from the only threat to winter-run chinook early in their lives. Many die for unknown reasons, and the committee also recommends identifying the other major threats to the eggs and very young fish. This would help gauge the relative benefits of various types of habitat restoration, such as augmenting the gravel where salmon lay eggs, releasing water pulses that flow through their redds or “nests,” and expanding floodplain nurseries for their young.
Likewise, dying early in life is far from the only―or even the main―threat to winter-run chinook. Other significant dangers include habitat loss and degradation, climate change, and stranding as flows fluctuate. Critically, water project operations have the potential to lessen these dangers.
Yet another issue the committee flagged is that managing Shasta Dam to benefit winter-run chinook could have unintentional impacts on other species. “Winter-run did not spawn below Shasta Dam historically so the condition we’re managing for is novel,” says committee member Rene Henery, California Science Director of Trout Unlimited.
Species that could be harmed include fall-run chinook, the mainstay of California’s commercial salmon fishery. For example, flows for winter-run chinook can also draw fall-run chinook to this spawning habitat, which dries out when the flows stop and can strand fall-run eggs.
“Fall-run are not listed but three years of fishery closures tells us they’re doing poorly,” Henery says. “There’s a massive need to take a more holistic approach to managing the Central Valley Project.” This includes considering threats to winter-run chinook throughout their life cycle as well as expanding the current narrow focus on endangered species to benefit a wider range of species.
OLD AND MIDDLE RIVER FLOWS
Water in the Delta naturally flows toward the Pacific Ocean but the export pumps disrupt this pattern, pulling water south via Old and Middle rivers. This can make these channels run backwards―that is, away from the sea and towards the pumps.
To help protect fish from being sucked south, water project operators aim to limit exports when fish are migrating through the Delta. Major triggers for curtailing Delta exports include salvage of imperiled fish at the pump facilities. However, while easy to measure, this trigger does not reflect the full impact of the unnatural southward flow of water on fish.
“Take at the pumps is not the only source of mortality,” UC Davis limnologist Sadro says. “The pumps draw fish into a zone of influence where mortality is inherently higher.” For example, fish predation is rampant in the south Delta.
To make water exports safer for fish, the committee recommends shrinking the pumps’ zone of influence. Possibilities for doing this include coordinating pumping with the tidal cycle in the Delta. “Most of the focus on fish protection in the Delta is on habitat restoration and water supply,” says committee member Jay Lund, a UC Davis (UCD) civil and environmental engineer and Vice Director of the UCD Center for Watershed Sciences. “But managing tidal flows could also improve in-Delta conditions for native fishes.”
Tides drive the dispersion of fish in the Delta and also shape their habitat, from salinity to turbidity (cloudiness) to food. Infrastructure such as strategically placed gates could dampen tides in the south Delta, reducing the environmental impact of pumping. Options for managing tides in the Delta are explored in a 2024 U.S. Geological Survey report called Physics to Fish: Understanding the Factors that Create and Sustain Native Fish Habitat in the San Francisco Estuary.
SUMMER/FALL DELTA SMELT HABITAT
Threats to Delta smelt include lack of suitable habitat during the summer and fall, when the fish are maturing. Notably, Suisun Marsh, a key nursery for Delta smelt on the western edge of the Delta, often gets too salty for the young fish during the dry season. When the committee began their study, the Summer-Fall Habitat Action reduced salt in Suisun Marsh by using tidal gates to push freshwater into the marsh, and by releasing water from reservoirs upstream of the Delta and pumping less water out of the south Delta.
This action sounds good in theory but is hard to assess in practice because so few Delta smelt remain in the wild. “How would we know if it worked?” asks committee member Denise Reed, a coastal expert at the University of New Orleans. “It’s a very, very difficult situation.”
The committee does have a possible solution: a model of the processes leading to the environmental conditions that Delta smelt need. Besides low salinity, these include the zooplankton that they eat as well as the turbid water that helps them find food while obscuring them from predators themselves. As one example of the many processes that control these conditions, flows can move fish food from the Central Delta toward the Suisun Marsh.
State and federal water project operators recently suspended the Summer-Fall Habitat Action’s reservoir releases and reduced exports that increase Delta outflows. This combination is called the Fall X2― a measure of the transition from salt to fresh water in the Delta―action. In suspending the Fall X2 action, the agencies cited U.S. Fish and Wildlife Service modeling suggesting that it is not a critical driver of Delta smelt survival.
Once again, however, the scarcity of Delta smelt makes the efficacy of Fall X2 difficult to assess. “A process-based model would give us some idea of whether Fall X2 is worth it or not,” says Reed, who is lead author on a 2021 report on how to develop process-based models to inform Delta smelt management. “It’s a lot of water.”
Knowing Fall X2’s worth matters despite the rarity of Delta smelt. State and federal fish and wildlife agencies are supplementing the wild population with hatchery releases, and the survival of these fish depends on restoring their habitat.
SCIENCE HUB
The Delta and its watershed are vast, and the water projects complex. “The scale is mindboggling,” says UC Law, San Francisco’s Owen. Adding to the complexity are the many state and federal agencies charged with supplying water and protecting fish.
The involvement of multiple agencies results in fragmented science. “Scientists and system operators are drawing on different assumptions, bodies of information, and models or versions of models while trying to manage the same system,” the committee wrote in their report. “That can easily lead to situations where different managers and regulators talk past each other, act at cross-purposes, or make mistakes that other entities’ knowledge or collaboration could have helped avoid.”
The committee recommends unifying Delta science in a multi-agency hub. “There’s a big opportunity to get everybody to paint a shared picture of the Delta,” says Trout Unlimited’s Henery. “Greater scientific alignment is sure to increase efficiency and reduce conflict.”
Balancing the needs of the environment and people may seem impossible as fish become increasingly imperiled and the water supply becomes increasingly uncertain with climate change. But the report shows there’s hope. “There’s incredible cause for optimism,” says committee chair Peter Goodwin, an ecosystem restoration expert at the University of Maryland Center for Environmental Science and former Delta Lead Scientist. “There’s a very strong commitment to science, and we haven’t exhausted all the options for what can be done.”
