River Temperatures and Survival of Endangered California Winter-Run Chinook Salmon in the 2021 Drought

The summer of 2021 was a grim one for endangered winter-run Chinook salmon in the Sacramento River. Close to 10,000 adult salmon returned to the river to spawn below Shasta and Keswick dams, the most since 2006. However, NOAA Fisheries models predicted approximately 75 percent of their roughly 31 million eggs died from water temperatures driven by the historic drought that shrank reservoirs across California. The interagency science team that monitors winter-run survival noted that 2021 was “one of the warmest and driest years on record.” Scientists believe that other factors including a deficiency of thiamine, or Vitamin B, in returning adult salmon reduced survival of fry that successfully hatched.

What was the main cause of mortality for winter-run Chinook salmon eggs?

Most of the eggs were killed by high temperatures in the 5-mile stretch of river where winter-run Chinook salmon lay their eggs below Keswick Dam. Keswick, about 9 miles below Shasta Dam, stops the fish from continuing upstream toward their historical spawning grounds in the mountain rivers near Mount Shasta. The dams force the fish to spawn in a low-elevation section of the river exposed to hot summer temperatures. Managers can strategically release water from Shasta Reservoir to keep the river cool enough for the salmon eggs to survive, but there is a finite supply. The river also carries water to people across California. While the fish successfully spawn in the section in years when there is enough cold water stored in Lake Shasta, the heat can kill their eggs in hot years. The 2020–2021 drought left less cold water in the reservoir to influence river temperatures downstream.

How do you know how many eggs died from temperatures in the river?

Biologists in helicopters observe where the endangered salmon deposit their eggs in nests, called redds, over the spawning season. Then scientists use highly detailed temperature models to analyze how releases of water from Shasta and Keswick dams move downriver. They combine that data with data on weather and air temperatures that often exceed 100 degrees F over the course of the summer. That tells them whether water temperatures at each redd rise beyond 53.6°F, the limit for survival and safe development of salmon eggs. Based on data from more than 100 spawning female Chinook salmon at Livingston Stone National Fish Hatchery, scientists estimate that the average redd contains about 5,310 eggs. They combine this information to estimate how many of the naturally spawned eggs survive the summer in the river.

How common is temperature-dependent mortality of eggs?

In about half the years there is little or no temperature-dependent mortality. This occurs when there is enough water in Shasta Reservoir to provide cold water—that is, cooler than 53.6°F—to protect winter-run salmon eggs. Salmon naturally lay thousands of eggs because their overall odds of survival is so low. That helps the population survive difficult conditions in the river and ocean, and take advantage when the conditions favor survival. In recent years, winter-run Chinook salmon have also gradually shifted to building their redds farther upriver. The redds are now usually more closely clustered in the few miles of river below Keswick Dam where temperatures often remain coolest. This has reduced the number of redds exposed to higher temperatures. Water managers have consequently reduced the stretch of river where they try to maintain temperatures protective of the eggs. 

How many winter-run Chinook eggs died due to high temperatures in 2021?

The NOAA Fisheries model estimated that 75 percent of the winter-run Chinook eggs died from river temperatures that were too high. This is a high level of temperature-dependent mortality, but not as high as the 77 and 86 percent of eggs that died from temperatures during the severe drought in 2014 and 2015, respectively. Without efforts to maintain temperatures for winter-run salmon eggs in the Sacramento River, the temperature-dependent mortality in 2021 would likely have been higher.

What other factors affected the survival of winter-run Chinook eggs and fry in 2021?

Biologists know that other factors beyond temperature also affect egg survival, including predation, disease, and other risks. Biologists lump these together as “background” mortality that similarly affects the eggs and newly hatched fish every year. Beyond any losses due to temperature, they estimate that this predictable mortality regularly kills about two-thirds of the offspring before they begin their migration downriver. 

Scientists have identified a new factor that affected the survival of winter-run Chinook salmon eggs and offspring in 2020 and 2021. That is an unusual deficiency of Vitamin B1, or thiamine, in returning adult Chinook salmon, which appears related to what they eat in the ocean before returning to spawn.

What is "thiamine deficiency?"

Biologists working in Central Valley salmon hatcheries noticed in recent years that the offspring of some adult salmon returning to hatcheries were swimming in circles and corkscrew patterns before dying. They traced this condition to a deficiency of thiamine in adult salmon returning from the ocean. Further research indicates that the adult salmon preyed heavily on anchovies that have been unusually abundant off the coast of California in the past few years. Anchovies carry an enzyme that breaks down thiamine. Scientists hypothesize that salmon in the ocean ate large amounts of anchovies, causing a deficiency of thiamine in spawning adults that is passed on to their offspring. While treatment in hatcheries can restore the health of affected fish, we currently do not have a way to treat fish spawning naturally in the river.

Thiamine deficiency causes juvenile Chinook salmon to lose ability to swim or to swim in corkscrew patterns. That reduces their survival in the wild.

What was the impact of thiamine deficiency on winter-run offspring?

Biologists tested adult salmon returning to hatcheries for thiamine levels in their eggs. They found that 80 percent of the adult female winter-run Chinook salmon sampled in the hatchery in 2021 had thiamine levels low enough to potentially cause mortality of their offspring. They can use those findings to calculate how many fish spawning in the river would be similarly affected. They estimate that about 44 percent of the newly hatched salmon that survived the elevated river temperatures and background mortality likely died from thiamine levels low enough to compromise their health and survival in the river.

How many winter-run eggs actually survived in 2021?

If returning adults spawned 31 million eggs and 75 percent died from river temperatures, that would leave approximately 7.75 million viable eggs. Background mortality then killed about two-thirds of the remaining eggs and fry. Finally, scientists hypothesize that thiamine deficiency likely caused the death of about half of those remaining fry before they reached Red Bluff Diversion Dam. That combination of factors led to the record low survival of only 3 percent of the emerging salmon, which is very close to the survival rate estimated from the number of spawning salmon and fry caught at Red Bluff Diversion Dam.

If thiamine deficiency is killing the salmon eggs, why try to cool the river?

Temperature-dependent mortality remains by far the largest factor in losses of winter-run Chinook salmon eggs when dry conditions contribute to higher temperatures in the river. Those years put the species at the greatest risk of extinction. The drought in 2014 and 2015 killed most eggs for 2 years in a row, before thiamine deficiency became an additional threat. The impact of thiamine deficiency may vary as the ocean and available prey species change, but warm river temperatures will remain an increasingly deadly reality for winter-run Chinook salmon. The difference is that while we have little influence on the ocean, we can affect river conditions. The decline of winter-run Chinook salmon and the toll of high temperatures in the river leave the species with little resilience against additional threats such as thiamine deficiency.

How will climate change affect river temperatures?

Temperatures in Shasta Reservoir and in the river downstream are likely to continue to increase with climate change, making the river an increasingly hostile place for winter-run Chinook salmon to spawn. As temperatures rise, water managers will increasingly struggle to maintain temperatures in the river below Keswick Dam that keep any winter-run eggs alive. At some point, rising temperatures will likely make that impossible. That is why NOAA Fisheries has proposed the crucial recovery strategy of reintroducing winter-run salmon to their historic spawning grounds in McCloud River that flows from cold springs on the flanks of Mount Shasta. Adding populations of winter-run salmon in their former habitat would spread the risk for this critically endangered species and will likely be the only way this native California salmon can survive climate change.

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How would reintroduction of winter-run Chinook affect water management?

The goal of reintroduction is to return the species to a secure habitat where the eggs and offspring could survive the warming expected to accompany climate change. Winter-run Chinook salmon have already reclaimed former habitat on Battle Creek, where the species was reintroduced beginning in 2019. The establishment of healthy populations of winter-run Chinook salmon in safer habitat could allow for more flexibility in managing water and temperatures for the displaced winter-run salmon now spawning below Shasta and Keswick dams.