New research published in Proceedings of the National Academy of Sciences has identified a critical vitamin deficiency as a major factor in the collapse of young salmon populations in California’s Sacramento River. Scientists now believe that a lack of thiamine (Vitamin B1) killed up to half of newly hatched fry from endangered winter-run Chinook salmon in 2020 and 2021.
The deficiency, linked to dramatic shifts in ocean food webs, may be accelerating long-term declines in both endangered and commercially valuable salmon runs across the West Coast. Adult salmon returning to spawn appear to have been heavily consuming anchovies, which produce an enzyme that breaks down thiamine. As anchovies surged in coastal waters starting in 2017—reaching near-record highs by 2021—salmon health began to deteriorate.
NOAA researchers and hatchery staff first detected the problem when they observed young salmon displaying erratic swimming behaviors and high mortality rates. Follow-up studies confirmed the link to thiamine deficiency. While hatcheries can now counter the problem with thiamine injections and egg treatments, wild salmon remain largely unprotected.
“This mystery has been especially difficult to solve because the source of the problem is in the ocean, but the effects show up in rivers and hatcheries,” said Rachel Johnson, a research fish biologist at NOAA’s Southwest Fisheries Science Center.
The findings point to broader concerns about ecosystem instability, as ocean conditions increasingly favor anchovy booms at the expense of biodiversity. Experts warn that the growing dominance of anchovies—paired with other marine stressors like algal blooms—may be concentrating nutritional risks across predator species.
“Salmon in California have endured one blow after another,” said NOAA’s Nathan Mantua. “There is really no safety net left. Any new impact could be the final blow.”
While thiamine deficiency has not been widely monitored, evidence suggests it may be more widespread than previously recognized. Scientists say early warning signs will likely come not from salmon health metrics but from ecosystem-scale changes detected through ocean surveys.
The findings underscore the need for integrated ocean monitoring and adaptive fisheries management as climate-driven shifts reshape marine food chains and threaten the resilience of already-vulnerable salmon populations.