This release includes data used to evaluate the structure and function of the Ross Lake and Diablo Lake food webs. This includes data on zooplankton density and production (zooplankton_density.csv and daphnia_region_production_biomass.csv), lake volume estimates used to expand zooplankton density and production data (lake_volume_estimates.csv), fish sampling (FishSampleEvents.csv), fish biological information including diets, age, and stable isotope analysis (FishFullData_formatted.csv, FishPreyLength.csv), scale back-calculations (salmonid_back_calc.csv, rss_back_calc.csv), fish energy density (calorimetry_processed.csv), stable isotope data for invertebrate end members (si_inverts.csv), and hydroacoustic sampling (ross_ha_densities.csv, diablo_ha_densities.csv). Fish and zooplankton sampling and stable isotope analysis were conducted by the USGS in 2019-2021, and hydroacoustics surveys were conducted in 2021. These data were also combined with fish data (species, size, age) from the National Park Service collected in 2005-2017 to evaluate fish size and age structure across a larger period of time. The bioenergetics model and information on running the model including inputs and outputs from our simulations and a user guide can be found the in FB4.zip folder. Please refer to the associated publications for additional details about data collection and processing.