Dam operations alter the hydrological regime of rivers with mostly negative effects on aquatic habitat. Sudden changes from high to low flow releases may cause detaching of pools from stream flows. Aquatic species may be stranded in these detached pools, called stranding pools, resulting in higher mortality of fish in those pools than in the channel. Here, we focus on quantifying the impact of flow releases of the Anderson Ranch Dam on the South Fork Boise River, which hosts bull trout an endangered fish species. We developed a 2-dimensional model of a 24 km long reach of the South Fork Boise River (Idaho, US) and simulated water surface elevations for different discharge releases from the Anderson Ranch Dam to delineate stranding pools as a result of discharge changes from high to low flows. Comparison between predicted and observed stranding pool locations showed good correlations. We analyzed frequency and size of stranding pools as a result of regulated flows. Our study shows that coupling high resolution maps with hydraulic modeling provides an important tool to quantify the effects and the risks of dam operation scenarios on fish stranding in those detached pools.