We modified, parameterized, and applied the individual-based model inSTREAM version 6.1 for lake-migrating populations of landlocked Atlantic salmon (Salmo salar) and brown trout (S. trutta) in a residual flow stretch of the hydropower-regulated Gullspång River, Sweden. This model description is structured according to the TRACE model description framework. Our aim was to model responses in salmonid recruitment to alternative scenarios of flow release and other environmental alterations. The main response variable was the number of large out-migrating juvenile fish per year, with the assumption that individuals are more inclined to out-migrate the larger they get, and that migration is an obligatory strategy. Population and species-specific parameters were set based on local electrofishing surveys, redd surveys, physical habitat surveys, broodstock data as well as scientific literature.•Simulations were set to run over 10 years, with sub-daily time steps, in this spatially and temporally explicit model.•Model calibration and validation of fish growth was done using data on juvenile fish from electrofishing.•The results were found to be sensitive to parameter values for aggregated fish, i.e., “superindividuals” and for the high temperature limit to spawning.