Background/Question/Methods The San Joaquin River historically sustained the largest spring-run Chinook Salmon (Oncorhynchus tshawytscha) run in California, estimated at ~ 200,000- 500,000 adult spawners. Due to heavy impacts to the river, including the building of levees, diverting of water for irrigation, pollution, and infrastructure including Friant Dam (est. 1942), the runs of Chinook salmon were completely eliminated. The San Joaquin River Restoration Program (SJRRP) was established to restore a self-sustaining population to the river. However, San Joaquin River water temperatures are a major concern for the success of the SJRRP because it is the extreme southern end of the Chinook salmon range in North America. The current Fisheries Framework for restoration goals for individual juvenile Chinook salmon growth rates and cohort recruitment are based on HSI models, which are not based on robust trophic bases for production and thermodynamic principles. We address this shortcoming by examining the spatial variation of water temperature and prey abundance, two critical variables for estimating the scope for production of cold water fishes. We focus on river macrophyte habitat, which is largely overlooked in approaches and models for estimating individual growth rates and cohort production. Results/Conclusions Water temperatures and prey abundance (density and biomass) vary widely among habitat types and sites within the San Joaquin River Chinook salmon rearing reaches. Invertebrate prey biomasses were significantly higher in macrophyte habitat compared to drift and riverbottom habitats, but these differences interacted with location and macrophyte species. Invertebrate sizes were also substantially larger in macrophyte habitat, likely reflecting opportunities for efficient foraging by juvenile Chinook salmon. Water temperature variation interacted with location and time, which affects the trophic and production efficiency of juvenile Chinook. These factors combined are being used to produce more suitable and realistic river and salmon restoration goals in collaboration with agency colleagues.
