The main contents of this data release are estimates of daily and annual abundances of federally-threatened natural-origin age-0 fall Chinook salmon (Oncorhynchus tshawytscha) passing Lower Granite Dam, Washington. Fish from this population are sampled as they pass Lower Granite Dam, but these sample data cannot be used directly to infer abundance because capture probability at Lower Granite Dam varies throughout the migration and because of the contemporaneous presence of unmarked hatchery-origin fish which are visually indistinguishable from natural-origin fish. Estimates of abundance were obtained by fitting a statistical mark-recapture model that integrated four related datasets: 1) the release/recapture data of passive integrated transponder juvenile salmon tagged as either part of a natural-origin fish survey or as part of hatchery monitoring efforts, 2) daily counts of fish sampled by the smolt monitoring program at Lower Granite Dam, 3) hatchery release data and 4) environmental and operational covariates of Lower Granite Dam. An integrated Bayesian mark-recapture model fit joint parameters for daily fish arrival and capture probabilities to these data to estimate the daily abundance of hatchery- and natural-origin fish. In addition to the main results, this data release contains the raw data used to the fit the models and related parameters such as daily capture probability estimates and daily abundances of hatchery-origin fish.