Winter Salmon in Hot Water

Biologists are learning why warm waters nearly decimated an endangered fish. Ula Chrobak goes with the flow. Illustrated by Laura Macias and Julie Ho.

Illustration: Laura Macias

A narrow band of orange on the horizon spreads into a gradient of pinks and purples as fish biologist Bill Poytress takes a boat out on the water. The broad but shallow Sacramento River is swollen from winter storms and milky-brown with dirt and debris. Poytress’s work starts at sunrise, 7:21 a.m. on that crisp January morning, when he and his crew of biologists dip four fish traps into the river. The traps are tethered to the Red Bluff Diversion Dam—a defunct concrete dam under which water and fish freely pass. The giant, rotating cones open their mouths to capture the river’s contents, funneling fish into tubs at their base.

At 10:50 a.m., Poytress and the other biologists come back to the traps to inspect the morning’s catch, noting the size and species of the fish inside. They survey the traps daily throughout the year; only raging downpours keep them away. Poytress then inserts the data into biweekly reports on the status of the river’s fish, some of which are threatened or endangered.

The crew works on the narrow steel catwalks that frame the fish-funneling cones. The catwalks bob and buckle from the thrashing of the turbid waters, but Poytress seems unfazed as he talks about the work done aboard these traps. A U.S. Fish and Wildlife biologist, Poytress monitors the river’s fish to aid their conservation. “We’re collecting the pulse of the river,” he says.

Fish biologist Bill Poytress at Red Bluff Diversion Dam. Photo: Steve Martarano, U.S. Fish and Wildlife Service

Recently, this monitoring revealed a mystery. The winter-run Chinook salmon, an endangered fish that swims upstream in winter and spawns below Keswick Dam in late spring, was struggling. In an average year, about 25 percent of their eggs hatch into young fish that swim back downstream, passing under the Red Bluff dam along the way. But in 2014, Poytress noticed that only about 5 percent of the fish eggs laid that year hatched and trickled down to his traps. His team had to figure out what was happening to save the salmon—already on the verge of dying out—from extinction.

Only one catastrophe could wipe out the entire population of winter-run salmon.

Now, scientists are learning that the factors influencing fish survival—such as water flow rates and temperature—are more complicated than previously thought. They’re finding that salmon are sensitive to multi-year droughts, like the one that hit California between 2012 and 2016. Climate change is causing more severe droughts and higher temperatures in California, threatening the salmon’s survival.

The fish will need more cold water to survive as its habitat warms. But California’s citizens compete with salmon for this same water, and their demands will increase with warmer temperatures and more drought. To save the Sacramento winter-run Chinook, scientists are using new research on its water needs to better manage the fish and prepare for an uncertain future.

It’s a tough job, but the fish are an “icon of the west,” says Garwin Yip, branch chief at the U.S. National Oceanic and Atmospheric Administration (NOAA) in Sacramento. “It would be a shame if our grandkids see salmon only on a piece of paper or hung on a wall.”

Illustration of an adult Chinook salmon. Image: NOAA Fisheries


A turbulent past

Like other West Coast salmon species, the Chinook travel from the Pacific Ocean and into freshwater streams to spawn. They lay their eggs in gravel nests called “redds”. Then the parents die, leaving the 7,000 or so offspring to hatch and fend for themselves. A couple of months later, the young fish, called “fry,” emerge from the redds.

After four to five months of dwelling in the river and eating insects, the fry change color from a spotted brown to silver and become smolt. The smolt swim downstream and out to sea, where they grow into adults and fatten up on squid, shrimp and other fish. Adult Chinook can grow to more than 100 pounds. Three years later, the full-grown fish return to the spawning grounds where they were born and repeat the cycle.

Graphic: Julie Ho

There are four “runs” of Chinook—fall, late fall, winter and spring—named for the season in which they return to rivers to spawn. The Sacramento River winter-run adults travel upstream in the winter and lay their eggs below Keswick Dam in late spring. The eggs start to hatch in summer; fry leave the redds between July and October. The fry feed along the river’s reaches, then swim downstream and enter the Pacific Ocean as smolts between January and March.

The Sacramento winter-run Chinook is the only summer-spawning salmon on the West Coast. Spawning in the hot California summer is risky, because the fish’s eggs need cold water to survive. But the fish was still able to thrive by spawning in cool mountain streams that feed into the Sacramento River. After the construction of Shasta Dam and its downstream partner Keswick Dam in the 1940s, however, the fish started struggling because the dams blocked adult salmon from swimming to these cold-water rivers and streams.

The dams decimated the four winter-run populations, named after their spawning streams: Little Sacramento, McCloud, Battle Creek and the Pit. Cut off by Keswick Dam, the populations dwindled and combined into one: the Sacramento. Listed as endangered in 1994, the Sacramento River winter-run Chinook are the last of their kind. Every summer, they return to a 44-mile stretch of the river between Keswick Dam and Red Bluff Diversion Dam to lay their eggs.

Shasta Dam in northern California. Photo: Bureau of Reclamation, shared on Flickr (CC BY-SA 2.0)

The existence of these salmon depends wholly on human actions. Shasta Dam gathers a reservoir of cold water from winter storms. From March to October, the U.S. Bureau of Reclamation releases the reservoir’s water downstream into the Sacramento River to protect the salmon eggs. If Reclamation doesn’t release enough water, the salmon’s eggs fry in the summer heat. Despite myriad other threats—habitat loss, water withdrawals and nonnative predators—spawning ground temperature largely determines how many salmon make it out to sea.

The federal and state fish and wildlife agencies monitor the number of adult carcasses that float downstream after spawning and the number of young fish that pass through the traps at Red Bluff to estimate how many survived from the eggs, known as “egg-to-fry” survival. Upstream, NOAA instructs Reclamation on the temperature needs of the fish so that Reclamation releases enough cold water. Until recently, NOAA recommended that the river needed to stay below 56°F for the eggs to survive and hatch.

So when egg-to-fry survival plummeted in 2014 and 2015, Poytress and his team were concerned. According to NOAA, water temperatures were adequate. The biologists at Red Bluff suspected that warmer temperatures, exacerbated by drought, were to blame. During those drought years, Reclamation had run out of cold water, which pools at the bottom of the reservoir, and was having trouble keeping the river cool. But a mystery remained: Why had so many fish died when water temperatures had mostly remained below 57 degrees? (Reclamation managers aimed for 57°F because they ran low on water; NOAA researchers thought many salmon would still survive.)

Graphic: Ula Chrobak

The sudden survival drop led some people to question Poytress’s data. Thaddeus Bettner, general manager of the Glenn-Colusa Irrigation District, thought the Red Bluff team might have underestimated the salmon by missing some sampling days. The district—which supplies water to farmers in the Sacramento Valley—hired a consultant to go through the data. Low fish numbers meant that the already drought-impacted district might get less water.

The district’s consultant estimated that, based on the water temperature in the spawning grounds, about 85 percent of the winter-run Chinook should have survived. The consultant asked Poytress to share his data, then sifted through each day’s observations at Red Bluff Diversion Dam and scrutinized instances where the biologists had been unable to get data. The farmers and irrigators used gaps in Poytress’s sampling to testify to state officials that Reclamation was not justified in reducing their water supplies.

But Poytress felt confident his team had not erred when it estimated that just 5 percent of the salmon had survived. Scientists at NOAA, who are responsible for the fate of the fish under the Endangered Species Act, needed to find out what was happening.

The physics of fish death

Benjamin Martin, a biologist at NOAA Southwest Fisheries Science Center in Santa Cruz, led the effort to solve the puzzle. Previously, he studied water fleas, which float in the same pond their whole lives, so the complex lifestyle of salmon was a new challenge. Using data collected from Red Bluff over the last two decades, he started looking at the relationship between egg-to-fry survival and temperature.

Martin found temperature still seemed to play a major role in survival. As the temperature at the spawning grounds increased, fewer fry survived. But he also noticed that fish in the river started dying at 54°F, instead of NOAA’s recommended 56°F.

Why was there such a big difference? Martin realized that NOAA’s figure had come from laboratory studies, in which scientists monitored eggs in a fish tank, then raised the temperature until they died. Those studies suggested most salmon would survive until the temperature hits 60°F.

There was clearly a discrepancy, but scientists still didn’t know why eggs needed colder water in the river than in the lab. Martin thought about how the two environments differed. In the wild, salmon bury their eggs in gravel nests, through which water flows slowly. But in the lab, the eggs were uncovered and water flowed freely past them. The water carries oxygen that embryos need to survive; slow-moving water carries less oxygen to eggs than a fast current, Martin realized. Warmer water also holds less oxygen. So, as water warms up and creeps more slowly past eggs buried in gravel, the eggs get less oxygen. This explained why salmon eggs in the Sacramento River had suffocated at a lower temperature than in the lab studies.

The team at Red Bluff was happy to have answers. “When this came out, the questions for us dropped off quite a bit,” says Poytress.

In this podcast, Ula Chrobak reports that warmer waters threaten a unique type of California Chinook salmon. Illustration by Laura Macias.

Lessons from the drought

Bettner is still skeptical. To him, “the jury’s still out on what the drivers were” for fish egg mortality in 2014 and 2015. Martin’s findings are a “theory,” he says, but he maintains that scientists should investigate other variables like predation and habitat quality in spawning grounds.

Bettner says he wants to help the fish, but he also must meet the competing needs of farmers. “How do we manage this [water] system holistically and try to meet all these competing needs?” he asks. “There are years when there are going to be trade-offs.”

In summer 2016, NOAA officials shared Martin’s findings with Reclamation at Shasta Dam. Reclamation then started releasing enough cold water to keep river temperatures at the spawning grounds below 54°F. The 2016 juvenile winter-run numbers were good: 24 percent egg survival, about average. But it’s not clear whether the 2016 survival was helped by an influx of more cool Shasta reservoir water, because other factors such as increased rainfall may have helped, says Yip at NOAA.

Still, NOAA and Reclamation scientists now have a clearer sense of what to do during droughts. Normally, Reclamation takes the amount of rainfall in each year and estimates how much water to store through the summer, making enough available to keep the Sacramento River cool. But in 2014 and 2015, they ran short on cold water, nearly decimating the winter-run Chinook. So for multi-year droughts, Reclamation is preparing long-term plans to store enough water for salmon to survive the dry spells.

“[The drought] was definitely a wakeup call in that we need to be thinking more long term—many years out,” says Poytress.

A rotary screw trap, which catches fish so biologists can study their health and abundance. Photo: Steve Martarano, U.S. Fish and Wildlife Service

On the January sampling morning, Poytress meets up with the two biologists—Samantha Adams and Leonard Cheskiewicz—monitoring the traps. To kill time, the three place bets on how many salmon they’ll catch: 26, 34 and 46, respectively. Then the biologists talk about the weirdest things they’ve found in the traps. “Probably a dead deer,” says Adams. “Rattlesnakes,” says Cheskiewicz, adding that they were alive. “A box of bok choy,” says Poytress. Apparently, the vegetables had fallen off a truck and landed in the river.

Soon, they’re back at one of the traps, surveying the day’s catch. After cleaning out the trap and dropping the fish into a “dope tub” with a mild anesthetic, Adams and Cheskiewicz measure each fish in millimeters.

Fish from each of the four Chinook runs. Biologists can tell which run the fish belong to by their length. Photo: U.S. Fish and Wildlife Service

They find small almond-sized silver salmon, some with yolk sacs from their eggs still attached. Because they’re so small and it’s January, the team knows they are newly hatched fall-run salmon, just leaving their spawning grounds. The 2016 winter-run salmon, which hatched months ahead of these tiny fish, have already moved downstream toward the Pacific Ocean. Cheskiewicz wins the bet: the traps snared 75 fall-run salmon that morning.

While the winter-run Chinook salmon did better in 2016, their struggle is not over. The 2014 and 2015 salmon that survived the drought will return to the Sacramento River in 2017 and 2018 to spawn below Keswick Dam. Poytress doesn’t know how the few fish that passed through Red Bluff in those years fared on the rest of their journey. The monitoring at Red Bluff is the most detailed on the river; there’s nothing like it to show how many fish got through the Delta and to the ocean. What’s more, during 2015 many of the fish leaving Red Bluff were sick, infected with parasites that could have reduced their resilience to threats downstream.

To give the fish a better chance, managers are trying to restore historic populations. Having more than one population of winter-run Chinook is important, Yip stresses. He recalls a 1991 incident when a train fell off its tracks and spilled toxic pollutants into the Sacramento River, killing much of the aquatic life. “If anything happens, only one catastrophe, it could wipe out the entire population of winter-run,” Yip says.

He proposes bringing back the Battle Creek winter-run Chinook population, which the dams wiped out decades ago, by stocking the creek with hatchery-raised salmon. But it’s not easy to get started. There are five agencies involved and a host of uncertainties such as where to put the fish, how to get them there, and how to prevent hatchery salmon from spreading disease. But Yip anticipates the effort will launch in 2018.

Fish futures

The winter-run scare has led to important developments in modeling the effects of climate change. Martin’s research produced an equation that could explain water temperature and flow needs of fish eggs worldwide. This means scientists could apply it to managing fish elsewhere, says NOAA biologist Eric Danner, coauthor of Martin’s study.

But climate change in California will lead to warmer temperatures and possibly more drought. If the fish are so tied to a delicate balance of temperature and flow, can they hang on for much longer?

Yip sighs and pauses before answering. “I’m going to keep fighting, and our agency is going to keep fighting until one or the other—recovery or extinction. We’re going to maintain that hope and keep plodding onward.”

The problem, says Poytress, is that California’s human population does not live within the limits of nature. Altogether, the state’s residents have rights to five times the water available in an average year. During drought, some landowners with “senior” water rights dating back more than a century can divert the same amount of water from the river as during wet years, leaving less for fish. Much of the water from Shasta Reservoir helps grow thirsty Central Valley crops like almonds and tomatoes. Those battles, says Poytress, are heated and ongoing.

He doesn’t know how to change society, but he has faith in fish. Usually, only about 0.2 percent of the winter-run salmon that swim downstream from Red Bluff return to spawn. But some years, inexplicably, it’s three times as much. He thinks researchers should study why the fish are so resilient, not just why they’re doing so badly.

“Even though populations are low, it’s very hard to eliminate them entirely,” Poytress says. “It’s really hard to kill the last fish.”

© 2017 Ula Chrobak / UC Santa Cruz Science Communication Program

Ula Chrobak

Ula Chrobak


B.S. (environmental science, soils and biogeochemistry track) University of California, Davis

Internships: Climbing Magazine and University of Colorado Boulder news office

When I go rock climbing, my imagination gets to work. I visualize the ancient seafloors that became limestone, and the molten rock that slowly cooled into the granite above me. I also look down, grabbing a handful of soil to examine its texture and color.

The humble soil beneath our feet has always compelled me. In my studies, I learned how the properties of soil reveal its origins, yielding a detailed story of the landscape. Outside class, I used my soil science knowledge to lead composting workshops.

My first job required me to write environmental impact reports for warehouses and housing subdivisions. That sole focus on development wasn’t what I wanted; I craved a career where I could view the environment from many perspectives. A lifetime of digging for stories awaits.

Laura Macias

Laura Macias


B.S. (biology, minor in Fine Arts) University of San Francisco
Internship: Ink Dwell Studio (Berkeley, California)

Laura Macias is a science illustrator and artist who uses bold imagery that features the beauty of the natural world to create interest in science. Growing up in Southern California, she spent a lot of time outdoors and became enamored with the ocean and sea life. Much of her inspiration emanates from the natural world and what she has learned from studying marine invertebrates. This summer she will be working with Ink Dwell Studio in the Bay Area. Ink Dwell is cofounded by Jane Kim, a fellow graduate of the Science Illustration Program. Laura will contribute to Ink Dwell’s mission of inspiring others to value science through beautiful works of art.

Laura’s website

Julie Ho

Julie Ho


B.F.A (pictorial arts) San Jose State University

Internship: Children’s Natural History Museum (Fremont, California)

An artist from the San Francisco Bay Area, Julie started her undergraduate studies in biochemistry but rediscovered her love for art halfway through and turned her concentration to creating art for science communication. During her time as an undergraduate she taught art classes in Los Altos, California, where she found her passion for children’s education. Influenced by the changing climate and its effect on life within it, Julie hopes to communicate local environmental issues through illustrations for science education.

Julie’s website