Survival of Endangered California Winter-Run Chinook Salmon in 2022

The production and survival of juvenile winter-run Chinook salmon in the Sacramento River in 2022 was the lowest on record. It was the third consecutive year of poor reproduction of the highly endangered species. The low numbers resulted from fewer adult salmon returning to spawn in the river below Shasta and Keswick dams, a deficiency of thiamine in the adults that reduced survival of their offspring, and factors that have not yet been identified.

High water temperatures in the drought-depressed river had killed many winter-run eggs in 2021 and earlier years. But these temperatures were not as much of a factor in 2022. Irrigators reduced their diversions, leaving more cool water to help keep winter-run eggs alive through the summer. NOAA Fisheries estimates that more than 80 percent of winter-run eggs survived temperatures in the river, much improved from about 25 percent that survived in 2021.

Introduction

Other factors unfortunately offset the improved survival of winter-run eggs in the river in 2022. First, fewer adults than expected returned from the ocean to spawn in the river.

Second, many adult salmon returned with critically low levels of thiamine, or vitamin B1. This compromised the survival of their offspring. Researchers estimate that about half of the young salmon that survived other factors likely died from lethally low thiamine levels soon after hatching. Since temperatures took less of a toll on eggs this year, thiamine deficiency emerged as a more significant cause of mortality. The number of surviving juveniles appears to be the lowest on record. About 200,000 juvenile winter-run salmon migrated downstream in 2022, less than the 558,000 in 2021. It was also less than the previous low of about 270,000 in 2014 during the previous severe drought.

While we understand the impacts of temperature and thiamine deficiency for 2022, other unexplained mortality sources emerged this year. Our current analytical tools predicted that the survival rate would be much higher than the roughly 2 percent egg-to-fry survival rate estimated by the most recent field data. We do not know what caused the further reduction in survival, but we are working with our counterparts at other agencies to understand the causes, especially considering the historic heat, flow, and habitat conditions on the river this year. 

The low production and survival of juveniles will likely lead to meager returns of adults in 2025 following their typical 3 years in the ocean.

Link to questions and answers on winter-run Chinook salmon survival in 2021

How did river temperatures affect winter-run Chinook salmon eggs in 2022? 

River temperatures for winter-run Chinook salmon during 2022 initially looked similar to 2021, given the limited cold water available in Shasta Reservoir. Estimates earlier in the year suggested that temperatures could kill half or more of the eggs in the river. However, lower releases from Shasta Reservoir conserved cold water, which was used to help moderate temperatures for winter-run over the course of the summer. This substantially reduced the toll that water temperatures took on the eggs. Tracking over the summer showed that eggs experienced less than 20 percent temperature-driven mortality in the river, indicating that these measures made a substantial difference in the number of eggs that survived.

What other factors affected the survival of winter-run Chinook salmon eggs and fry in 2022?

Biologists know that factors beyond water temperatures affect survival of young salmon. The factors include predation, disease, and other drivers. When nests and the resulting offspring are crowded together, fewer offspring generally survive. Habitat limitations also reduce the survival of offspring. Biologists estimate that these combined sources of mortality kill about two-thirds of the winter-run offspring as they migrate downriver.

Scientists suspect that thiamine deficiency driven by ocean conditions may have long affected salmon survival at some level before it was identified in the Central Valley in 2020. The difference today is that the critically endangered winter-run Chinook salmon individuals are more vulnerable to environmental factors that affect their survival. This manifests in population-level effects that worsen over time because the species now lacks the resilience to withstand such variations in annual survival rates.

What is “thiamine deficiency”?

Thiamine deficiency affected survival of winter-run Chinook salmon offspring in each of the past 3 years. This deficiency of Vitamin B1, or thiamine, in returning adult Chinook salmon, appears related to what they eat in the ocean before returning to spawn. Anchovy numbers have been extremely high off the California Coast in recent years, providing plentiful food for adult Chinook salmon on their way back to rivers. The problem is that anchovies carry an enzyme that degrades thiamine. This reduces thiamine levels in the salmon that consume them in the ocean, and the reduced levels are transferred to their offspring. Scientists first recognized this threat in 2020. 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 and were unable to eat, and left untreated the symptomatic fish died. Low thiamine levels killed an estimated 21 to 23 percent of fish in 2020, and 44–-49 percent of the fish in 2021.

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

Can we do anything about thiamine deficiency?

Fish health experts at salmon hatcheries realized that immersing affected juvenile salmon in a thiamine bath quickly reversed the effects. They also began injecting returning adult females with supplemental thiamine, which reduces the effects of thiamine deficiency on their offspring. Researchers have also treated some returning wild adult Chinook salmon the same way before releasing them back into the wild. For example, some adult winter-run Chinook salmon returning to Battle Creek in Northern California were collected and transported around barriers. They were released to spawn in upper reaches of the tributary where water remains cooler in the summer. This gave researchers an opportunity to treat the adult females with thiamine before releasing them. They plan to use parentage-based tagging to identify offspring of the treated fish when they return as adults 2 to 3 years later. This will tell us whether the treatment is effective in improving the reproductive success of fish in the wild. Biologists are also considering whether it would be practicable to treat returning adult salmon that spawn in the Sacramento River below Keswick Dam.

How did thiamine deficiency affect winter-run offspring in 2022?

Biologists test adult salmon returning to hatcheries for thiamine levels, which indicates the likely effect on their eggs. They found that about 93 percent of the adult female winter-run Chinook salmon sampled in the hatchery in 2022 had low thiamine levels and 71 percent of the adult female winter-run Chinook salmon sampled in the hatchery in 2022 had critically low thiamine levels. Those levels are low enough to cause mortality of their offspring. They expect that a similar number of fish spawning in the river would have been affected. The juvenile salmon remain exposed to the impacts of thiamine deficiency, which compromises their swimming ability and makes them more vulnerable to predators and other threats. Initial estimates indicate that thiamine deficiency killed about half of the newly hatched salmon that survived the river temperatures and background mortality in 2022.

What is causing the boom in anchovies that appears to be causing thiamine deficiency in salmon?

Scientists have been asking this question for decades but are now getting closer to understanding the factors through recent research. Initial indications are that anchovies hatched from eggs in good conditions and had plentiful nourishing food available since 2015. That, and perhaps a lack of predation from diminished stocks of other small pelagic fish species, allowed many more anchovies to survive through the earliest stages of life which is the most challenging part of their life cycle. The result is that anchovy numbers along many parts of the California Coast are much higher than they had been in prior years. This research is ongoing.

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

Typically, when dry conditions contribute to higher temperatures in the river, temperature-dependent mortality has been the largest factor in losses of winter-run Chinook  salmon eggs. Those years put the species at the greatest risk of extinction. The drought conditions in 2014 and 2015 killed most eggs for two consecutive years, before thiamine deficiency became an additional threat that challenged winter-run survival. The impact of thiamine deficiency may vary as the ocean and available prey species change. But river temperatures will remain an increasingly deadly reality for winter-run Chinook salmon. This is especially true as climate change continues to influence temperatures and precipitation. The difference is that while we have little influence on the ocean, we can affect river conditions through management of water storage, flows, and diversions. 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 common is temperature-dependent mortality of eggs?

In about half the years there is little or no temperature-dependent mortality. This occurs when the water in Shasta Reservoir is cooler than 53.6°F, which protects the eggs. Salmon naturally lay thousands of eggs because their overall odds of survival are so low. In recent years, winter-run Chinook salmon have also gradually shifted to building their nests farther upriver. They 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 nests exposed to higher water temperatures further downstream. Water managers have consequently reduced the stretch of river where they try to maintain temperatures protective of the eggs. 

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

Biologists in helicopters observe where the endangered salmon deposit their eggs in nests over the spawning season. Then scientists use highly detailed temperature models to analyze how water releases from Shasta and Keswick dams move downriver. That tells them whether water temperatures at each nest rises beyond 53.6°F, the threshold for survival and safe development of salmon eggs.

How many winter-run Chinook salmon eggs died due to high temperatures in 2022?

Reduced releases from Shasta Reservoir and reduced diversions by irrigators helped maintain suitable river temperatures in a limited portion of the winter-run spawning habitat throughout much of the 2022 spawning season. Generally, water temperatures turned out to be lower than had been forecasted in May. They often remained just below the critical temperature for incubating eggs in the spawning reach of the river.

NOAA Fisheries’ Southwest Fisheries Science Center estimates that about 17 percent of eggs died from temperature-dependent mortality this year. This is less than the estimated 90-plus percent mortality that would have resulted had the voluntary reductions not been adopted. It is also much less than the 75 percent mortality caused last year by high river temperatures. This is a credit to water users who reduced diversions so that more water would remain available to the endangered fish.

How will climate change affect river temperatures?

Temperatures in Shasta Reservoir and in the Sacramento River downstream are likely to continue to increase with climate change. This will make the river an increasingly challenging 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 winter-run eggs alive. NOAA Fisheries has proposed a crucial recovery strategy that calls for reintroducing winter-run salmon to their historic spawning grounds in the McCloud River that flows from cold springs on the flanks of Mount Shasta. Adding populations of winter-run salmon in their former habitat is a key recovery action. It would spread the risk for this critically endangered species and will likely be the only way this native California salmon can survive climate change.

How do repeated drought years affect salmon?

Winter-run Chinook salmon maintain resilience to changes by spreading risk across multiple generations that return to West Coast Rivers in consecutive years. Most juvenile winter-run Chinook salmon that make it to the ocean will typically return 3 years later. While poor river conditions could affect one year-class of returning salmon, the species has two more years to make up for it. However, when drought conditions continue over multiple years, the species does not get a chance to bounce back. Instead, the poor conditions affect generation after generation of fish, leaving fewer and fewer returning adults to spawn. That makes it even more essential, after two or more hard years, to protect the third year of returning fish and their offspring. The offspring from 2022 are the third year with low reproductive success, and the numbers of offspring were the lowest ever. We are fortunate to have some surviving fish. We need help to promote their survival and ensure that some salmon return as adults so the species survives.

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

The goal of reintroduction is to restore access to historical 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 into historical habitats could allow for more flexibility in managing water and temperatures for the displaced winter-run salmon now spawning below Shasta and Keswick dams.