An image of a blurred flowing river.
Flowing from the Klamath Mountains to the Pacific, California’s Smith River is a critical habitat for salmon and trout species.  Photo: iStock.

Following the Flow

Rausser College researchers advance knowledge of California’s sensitive freshwater ecosystems.

California landscapes are shaped by our desire to control the absence or abundance of one key natural resource: water. More than a century ago, water from the Owens River was diverted to promote growth in the city of Los Angeles. The Tuolumne River was dammed to create the Hetch Hetchy Reservoir, supplying water to San Francisco. The Central Valley Project and California State Water Project both use water from the Sacramento-San Joaquin Delta to provide municipal water for more than 23 million people and irrigate California’s largest agricultural region.

After being assessed by graduate student Brian Kastl, a juvenile coho salmon is returned to Willow Creek, a tributary of the Russian River.

Photo: Sean Perez

The state’s complex, multipurpose network of dams, reservoirs, and other facilities forms one of the most elaborate water management systems in the United States—one that is under stress as climate change results in extreme weather events like extended drought and excessive precipitation.

Stephanie Carlson, a professor of fish ecology and A.S. Leopold Chair in Wildlife Biology, worries that this variability will make it harder for California’s water managers to meet urban and agricultural demand while also ensuring the health of the state’s freshwater ecosystems.

“We saw extreme competition for California’s limited freshwater during the 2012-2016 drought,” she says. “This year, in contrast, we are seeing storm after storm and widespread flooding. This extreme variability is a major challenge for managing California’s aquatic ecosystems and the wildlife and people they support.”

Carlson’s research into California’s freshwater woes aligns with that of her colleagues Ted Grantham and Albert Ruhi. Together, these faculty members lead the Freshwater Research Group, a consortium of researchers who regard freshwater as our most important natural resource and work to understand, monitor, and promote its resilience.

Connected Cycles in Crisis

“Humans exert tremendous control on California’s water cycle,” says Ruhi, who studies how freshwater ecosystems respond to drought, dams, and other stressors. “Most of the state’s precipitation falls in the Sierra and ends up in the Sacramento-San Joaquin Delta—the hub of California’s water supply, supporting two-thirds of the state’s population and millions of acres of farmland. It’s a very managed system.”

Three researchers in waders standing in a creek.

Left to right: Stephanie Carlson, Albert Ruhi, and Ted Grantham lead the Freshwater Research Group.

Photo: Jim Block

Ecosystems that previously existed in an unaltered state are now burdened by the water infrastructure that sustains our urban areas, and environmental factors like drought and climate change further stress these sensitive habitats and the species that depend on them. A 2011 assessment found that only about 20 percent of California’s freshwater and estuarine fishes can be considered stable—a finding that Carlson considers to be an indicator of a steady decline in ecosystem health.

Much of Carlson’s research focuses on migratory species of wild salmon and steelhead trout, which were historically abundant in many of California’s waterways. Every month of the year, salmon migrated up the Sacramento and San Joaquin Rivers and connected tributaries to breed; their offspring used the same waterways, migrating to the ocean to feed and grow before returning to breed several years later, thereby completing the life cycle.

The National Oceanic and Atmospheric Administration (NOAA), the federal agency responsible for stewarding the nation’s fisheries and marine ecosystems, reports that dams block steelhead from reaching more than 80 percent of their historical spawning and rearing habitat in California’s Central Valley. Carlson says lost access to historic habitat is a major obstacle to salmon recovery. Fish that relied on these cooler, higher-elevation waters had distinct patterns of growth and migration age compared to lower-elevation fish. According to Carlson, those life histories—or paths through the life cycle—are rare in the context of today’s highly modified rivers. “Long before we lose species, we lose the many forms of a species,” she says. “Those many forms—such as salmon populations that spend different amounts of time in freshwater before migrating, or others that return to breed at different ages—provide options in an increasingly variable world.” 

"California’s freshwater ecosystems are in a state of crisis."
– Ted Grantham

“California’s freshwater ecosystems are in a state of crisis,” says Grantham. “We’ve documented steady and consistent declines in ecosystem health since the 1970s, and those trends are expected to continue.” In the state’s North Coast region, where rivers have fewer dams than those in the Central Valley, Grantham has still observed human impact on freshwater ecosystems, as people divert water from streams to their lands for agricultural and domestic use.

While an individual diversion might not dry out a stream, cumulative impacts are worrisome, he says, especially during dry years when water supplies are naturally limited. During these periods, even small reductions in streamflow can negatively affect ecosystems in a multitude of ways. Low flows directly limit the availability and quality of habitat for wildlife and can act as a barrier to migratory fish at various points during their life cycle. Depleted streamflow can also increase water temperatures, which Grantham says may push species over their range of tolerance and lead to toxic algae blooms.

Kyle Leathers, a graduate student working with Ruhi, studied temperature variations in the Kings River in the southern Sierra Nevada and found 26 percent of cold-water habitat in the watershed could be lost to the effects of climate change. Those effects threaten more than a quarter of the aquatic species in that region (potentially altering the region’s entire food web) and could reverberate throughout the state’s freshwater ecosystems.

Monitoring Change

The Freshwater Research Group is working to understand historical conditions and monitor changes to predict what the future may hold for California’s fragile freshwater ecosystems. Some of the research also involves mimicking projected conditions in a controlled environment to assess outcomes.

A researcher in waders sitting on the banks of a curved artificial river

Graduate student Kyle Leathers conducting water flow experiments in artificial channels at the Sierra Nevada Aquatic Research Laboratory.

Photo: Albert Ruhi

In a recent experiment conducted at the Sierra Nevada Aquatic Research Laboratory—a station managed by the UC Natural Reserve System—Ruhi manipulated water levels in artificial streams to simulate the long-term effects of predicted climate trajectories. The results were unexpected: rather than causing an across-the-board decline in ecosystem biodiversity, low water levels in the artificial stream increased the development rate and shifted the timing of the metamorphosis and emergence of aquatic insects, which could have cascading effects on predators like lizards, birds, and bats. “You can find climate impacts on one species, but when you look at the ecosystem as a whole, new responses emerge,” Ruhi says. “We must consider not just how individual species respond, but also whether the interactions among them change—including in adjacent ecosystems.”

While a low flow can permanently alter a stream, Grantham says it’s important to remember that most of California’s rivers and streams are naturally intermittent, and they are capable of supporting a rich diversity of plants and animals and providing water for people. However, Grantham says, very few long-term flow records from intermittent streams exist. “Knowing the natural hydrology of intermittent streams can help researchers understand their sensitivity to human stressors, their role in supporting terrestrial and aquatic biodiversity, and how these ecosystems may change in the future.” 

“Long before we lose species, we lose the many forms of a species.”
– Stephanie Carlson

Since 2019, Ruhi has documented instances of intermittent streamflow throughout Pinnacles National Park, where rivers and streams provide water and refuge to an array of fish, birds, mammals, amphibians, and invertebrate species. “We know that the watershed is intermittent, but thought that some sites would hold water year-round,” he says. “Last year, to our surprise, most of the sites dried up.” The research shows that drought might degrade the few perennial freshwater habitats of an otherwise hot and dry region.

Carlson and members of the Freshwater Research Group have found that salmon breeding in intermittent streams encounter different conditions than those in year-round streams, which likely has consequences for size and migration timing. “Life-history diversity is now recognized as a key ingredient for a resilient salmon complex,” she says. “Maintaining a diversity of river habitats—including some that flow year-round and others that are seasonal—contributes to resilience because some populations perform best during wet years and others do better during dry years.” 

Watershed-level planning

Last November, federal regulators approved the removal of four hydroelectric dams on the lower Klamath River in California and Oregon after finding that the environmental benefits far outweigh the impact. Billed as the largest dam removal in the world, NOAA officials estimate that several threatened species of native fish—including coho salmon, Chinook salmon, and steelhead trout—will regain access to 400 miles of habitat.

But projects of that scale aren’t always feasible. “Some dams won’t go away anytime soon because they provide critical flood control or hydropower,” says Ruhi. “However, even then there are opportunities to manage them better.”

In recent years, the National Park Service and the U.S. Bureau of Reclamation have examined  the effects of water releases from Arizona’s Glen Canyon Dam. The timing and volume of water needed for hydropower generation leads to fluctuations in river water level, a change that can be deadly for aquatic insects, says Ruhi. When river flows drop after a hydropower release, insect eggs laid along the high-water mark typically dry out and die within hours. 

"Even when rivers are significantly altered, we can still increase ecological integrity."
— Albert Ruhi

On weekends, when electric demand is low, water managers have tested releasing a steady flow of water from the dam to minimize disruption. Ruhi and others evaluated the results of this test and found that the alternative release schedule improved egg-laying conditions for aquatic insects, which benefited the food web by providing an abundance of prey for fish. “They tweaked their operation effectively,” he says, “showing that even when rivers are significantly altered—in this case by one of the nation’s largest dams—we can still increase ecological integrity.”

Similarly, a renewed focus on life-history diversity in fishes is informing a more holistic approach to the management of California’s freshwater ecosystems. Carlson says that there is increasing recognition that diverse life-history portfolios contribute to the ability of salmon populations to survive environmental variability. “While much effort has gone into restoring rivers and streams to increase the amount of habitat available to fish species, there is potential to build on these efforts—to not only increase the number of fish but also increase their resilience,” she says.

Grantham’s research and outreach work focuses on identifying how policymakers can incorporate ecological principles in water management. “One of the most important things that state lawmakers could do is to formally recognize environmental water needs,” he says, “but  California continues to prioritize human consumptive uses—especially for agriculture—over ecosystem health.” 

Like California’s newly implemented groundwater management plans, Grantham says watershed-level planning may help stakeholders hash out how to sustainably allocate water under unpredictable and variable conditions. “There will still be politics and conflicts over these decisions, but a formalized process for community-driven water allocation planning would be a helpful step forward in our state.”