NOTEBOOK FEATURE: California’s unnatural river flows threaten aquatic life—here’s a (partial) fix

By Robin Meadows

As a New York Times columnist once quipped, “California’s water system might have been invented by a Soviet bureaucrat on an LSD trip.” The system was engineered in the 1900s to capture winter rain and spring snowmelt in vast reservoirs and then send this water to cities and farms via thousands of miles of canals, pipelines and tunnels.

While this system suits many people, it doesn’t suit fish, frogs and other river life. Many California waterways are regulated by reservoirs that release water for supply, flood control, and hydropower, resulting in river flows that are far from natural. Now there’s a movement to reinstate the seasonal flows that native species depend on.

“The idea of mimicking a natural flow regime is not rocket science and it’s not new,” says Sarah Yarnell, a river ecosystems expert at UC Davis. Like many innovations, it’s just taken a while to start percolating into the mainstream.


Foothill yellow-legged frog. Photo by U.S. Fish & Wildlife Service.

California’s river flows historically varied widely from year to year, from very wet to very dry and—importantly—everything in between. “Today we’re bouncing between extreme wet and dry, and we often manage our rivers to be really dry in most years,” Yarnell says. “We’re losing the occasional intermediate conditions that allow species to thrive in most years, so they’re just hanging on.” She likens this to always feasting or fasting rather than eating a healthy moderate diet much of the time.

Rivers also swelled and ebbed with the seasons. The rainy season onset typically brought fall freshwater pulses that let adult salmon know when it was time to migrate upstream to spawn. Flows then peaked in the winter, scouring out river channels and inundating floodplains where baby fish grow up; and finally dropped off gradually over the spring, as snowmelt ended and many runs of young salmon made their way toward the ocean.

During the foothill yellow-legged frog’s breeding season, flows must recede slowly enough to avoid desiccation of eggs. The red line shows a typical managed flow pattern; the blue lines show a range of natural flow patterns. Figure by Sarah Yarnell.

But now flows are typically at constant low levels much of the year, punctuated by occasional sharp spikes from winter to early spring in wetter years, when reservoirs release water to make room for snowmelt. The natural gradual dropoff of snowmelt is then captured in the reservoir rather than running downstream. This unnatural flow pattern causes a mismatch with the life cycles of river species.

To give just one of many examples, managed flows can leave foothill yellow-legged frogs literally high and dry. These at-risk frogs, which live in the Sierra Nevada as well as the central and northern Coast Ranges, are among the few that breed in rivers instead of ponds.

“Adults tuck their eggs into little velocity shelters, such as on the downstream side of a rock,” Yarnell says. The tadpoles then grow up in shallows along the river edge.

But today’s abrupt drop in spring water levels can dry out the eggs of foothill yellow-legged frogs, or abrupt spikes in flows can flush away the tadpoles, which are “terrible swimmers compared to fish.”

Functional flows (red line) mimic key components of natural flows (blue line). Figure by Sarah Yarnell.

Yarnell has worked with natural resource agency scientists and hydroelectric dam operators in the northern Sierra Nevada to release spring flows in a series of frog-friendly declining steps rather than the abrupt decreases that can dry out frog eggs . “Once one project shows how it can be done, there’s something for others to follow,” she says.

She’s also part of a team developing state guidelines, called the California Environmental Flows Framework, for managing rivers more naturally. The basic concept is to create instream flows and reservoir releases that have certain aspects of historical flow patterns, which will make rivers work more like they used to; scientists call these functional flows.

The state already does something similar in some rivers for salmon, releasing fall pulses to entice spawning adults upstream for example. Instituting a more complete set of functional flows would extend this stewardship more widely. “The idea is to improve flow and channel conditions for all native species,” Yarnell says.

This approach is catching on. Notably, the California Department of Fish and Wildlife is beginning to apply the state environmental flow guidelines in their Instream Flow Program, which aims to maintain healthy conditions for aquatic and riparian species. “It’s exciting to see some implementation,” Yarnell says. “There’s lots of opportunity.”


Functional flows can be established with the management currently common on many rivers, specifically fixed minimum flows that vary seasonally as well as across wet or dry years. But Yarnell and many other scientists favor a more flexible approach: granting rivers an annual amount of water, such as a percentage of inflows to reservoirs, that varies depending on how wet a given year is. This volume of water could then be released in more natural flow patterns over the year to benefit native species.

This strategy, called an environmental water budget, is “one of the best ways to implement functional flows,” Yarnell says.

Dry riverbed of the San Joaquin River east of Los Banos, California, in November 2021. Photo by USACE EWN.

Flows budgeted for rivers can be safeguarded by appointing independent ecosystem managers. Tom Johnson fulfills this role for a stretch of the San Joaquin River, which has both a water budget and an independent restoration administrator as part of the 2006 settlement agreement that resulted in the San Joaquin River Restoration Program (SJRRP).

The San Joaquin River had been troubled since the U.S. Bureau of Reclamation built Friant Dam in the 1940s to supply irrigation water as far as Bakersfield, which is 200 miles south. The Bureau diverted so much water to agriculture that 60 miles of the riverbed regularly ran dry and spring-run Chinook salmon, which are now listed as federally threatened, disappeared. Launched in 2009, the SJRRP is charged with restoring spring-run Chinook while minimizing adverse impacts on agriculture and other water users.

Besides getting only a minimum volume of water, many rivers get flows that are released on a fixed schedule. In contrast, the SJRRP’s river water budget gives Johnson the flexibility to adjust flows to meet the needs of the salmon, which include cold water.

Keeping the San Joaquin River cool enough for spring-run Chinook is a challenge: after returning from the ocean in the spring, adults wait until fall to spawn. While the fish once summered in cool mountain streams, Friant Dam blocks access to these historical spawning grounds. Today these salmon are stuck in the Central Valley all summer, where temperatures can be blazingly hot.

This is where Johnson’s role as restoration administrator is key. “Rather than having a rigid, prescribed flow, it can be tailored to conditions,” he says, adding that examples include releasing more water when it’s really hot. “A water budget provides the opportunity to do more biological good with the same volume of water.”

Spring-run chinook. Photo by SJRRP.

The caveat for the SJRRP is that environmental flows can be as low as one-tenth of those stipulated in the settlement agreement. This is due to unanticipated seepage into the almond and pistachio orchards planted in the San Joaquin River’s former floodplains; seepage can raise the water table, making the soil too soggy or salty for these high-value crops. The Bureau of Reclamation is buying seepage easements and installing drains in agricultural lands, and anticipates releasing full environmental flows in 2030.

Even with just a small fraction of the water budgeted for it, the SJRRP has already had tremendous success. “We’ve had spring-run come back to the river to spawn for the first time in 65 to 70 years,” Johnson says. “We have had as many as 400 San Joaquin-born fish return in a single year—it’s fantastic.”

Johnson is excited to see what the future holds for environmental water budgets and independent ecosystem managers. “Once seepage constraints are alleviated and we can really use the restoration flows as envisioned in the settlement, I have really high expectations and hopes,” he says. “If we can do it on the San Joaquin River, we could test it on other rivers—there’s huge potential to make better use of water in California.”


Jeffrey Mount, a river scientist and Public Policy Institute of California water policy fellow, says the state could use a complete rethink on river stewardship. “Now flows are Environmental Species Act-driven so we meet the letter of the law and extract all the rest—this makes the environment a constraint rather than a priority,” he says.

“Our focus is on trying to create Disneylands for endangered species, which ignores the fact that environmental restoration would also benefit the many other species that should be listed,” Mount continues. Up to half California’s freshwater fish species are on a pathway to extinction by the end of the century, according to a 2023 California WaterBlog post by renowned fish experts Peter Moyle and Robert Leidy.

Rivers suffer most during California’s frequent dry years, when water users grab every drop they can. Ecosystem managers could prepare for the state’s inevitable low rain and snow periods by, for example, saving some of the water allocated to rivers in wet years to keep them flowing well in dry ones.

“We always act surprised when drought shows up, with ad hoc actions to try to protect species and ecosystems,” Mount says. “One place to start is to give the environment a water budget and someone to manage it, especially during drought—we should plan for it, rather than react to it.”

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