Multiple Stressors in the San Francisco Estuary and Watershed: Effects of high temperature and low oxygen on the survival and physiology of early life stage Chinook salmon

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Education, Training and Public Information

Delta Science Fellowship 2020

Fellow: Annelise Del Rio, PhD Student, UC Davis
Research mentor: Anne Todgham, University of California, Davis
Community mentors: Rachel Johnson , NOAA Southwest Fisheries Science
Center; Ben Martin, NOAA Southwest Fisheries Science Center; Josh Israel, Bureau of
Reclamation Bay-Delta Office

Why this research matters

Chinook salmon in California’s Central Valley are at risk of extinction, and face multiple
challenges including competition with humans for water resources, habitat loss, watershed
degradation, and negative effects of hatchery propagation. Climate change is expected to add a
new layer of stressors for Chinook salmon, including higher water temperatures and decreased
oxygen concentrations in waterways. In order for natural resources managers to help support
salmon recovery, it will be important to understand how these climate-related factors affect
salmon, in particular in combination with each other.


The aim of this project was to investigate the effects of elevated temperature and low oxygen
encountered by early life stage salmon. The project included both a field study and a laboratory
component. Del Rio and colleagues created 24 artificial salmon nests (known as redds) containing
freshly spawned salmon eggs and equipment to log the water conditions. They then monitored the nests
to see how many fish hatched. Using the field data, the researchers then developed a model to
determine which environmental variables—such as temperature, oxygen, water flow and depth, and
substrate size—best predicted hatching success.

To study how salmon are affected by warming, low oxygen, and the combination of stressors she also
conducted a laboratory study where salmon eggs were exposed to one or both stressors at different
developmental stages to investigate the short and long-term effects of each stressor.


The field study found that overall, hatching success was low and variable. The results indicated that both
egg quality and environmental conditions were important in hatching success. They found that the
model of environmental variables could explain approximately 40% of the variability in hatching success.
Through the data loggers, the researchers were able to collect valuable fine-scale data for temperature
and dissolved oxygen, capturing greater variability than they would have had with manual
measurements. The study showed that in addition to temperature, other water quality variables such as
hypoxia are important in spawning success.

The laboratory study found that salmon embryos were most sensitive to the combination of warming
and low oxygen shortly before hatch. Exposure to warming and/or hypoxia during embryonic stages also
had lasting effects on the physiology and development of salmon during larval and juvenile stages, even
when the stressors were no longer present, indicating sublethal effects may be important to consider.

Management Applications

The study identified water quality variables that can be targeted in salmon management plans in
addition to temperature, especially plans that aim to support early life stages of salmon in their
freshwater habitat. Differences in water quality and survival observed across salmon spawning habitat
can be used to identify areas for spawning habitat restoration efforts. The laboratory study found that
salmon embryos were most sensitive to stressors shortly before hatching, which could inform water
management strategies that can allocate water for salmon embryos when they need it most. The long-
term effects of developmental exposure to stressors also suggest that sublethal effects should be
considered for salmon in the Bay Delta system in addition to lethal thresholds for water quality.

Select Publications and Presentations

Del Rio, A. Critical windows in Chinook salmon development: Differential sensitivity to warming and
hypoxia during development and long-term effects of developmental exposure. American Fisheries
Society Annual Meeting, Reno, NV 2019.
Del Rio A. 2019. Critical windows in Chinook salmon development: Differential Sensitivity to warming
and hypoxia during early development. State of the San Francisco Estuary Conference. Oakland, CA,
October 2019.
Del Rio, A. 2020. American River Chinook Salmon Survival in Relation to Redd Water Quality: The Role of Spatial and Temporal Variability. American Fisheries Society Annual Meeting. Virtual, September 2020.