Hydroelectric development and fish entrainment pose significant threats to fish populations, thereby exerting a profound impact on ecosystem functioning within human-affected river systems. This study addresses the potential loss of numerous fish species from the reservoir due to hydraulic diversions. An approach to assess both physical habitat and fish entrainment risk in the Williston Reservoirs was introduced, with a focus on two fish species: bull trout (Salvelinus confluentus) and kokanee salmon (Oncorhynchus nerka). The modeled results illuminate a seasonal fluctuation in forebay entrainment risk resulting from the operated intakes. The entrainment risk for kokanee in summer is highest, followed by fall and winter, while spring has the least entrainment risk. Modeled results also suggest that kokanee entrainment risks increase with flow rate of the operated intakes. Due to the fish entrainment risk, kokanee density and population decrease during the reservoir regulation, potentially leading to a reduction in the overall kokanee population over time. Conversely, the entrainment risk for bull trout remains limited, and its density and population appear to be unaffected by reservoir regulation and the subsequent fish entrainment risk. These insights hold relevance for optimizing operations in different seasons, and provide valuable input for informed decision-making aimed at mitigating the risks associated with fish entrainment.