AbstractUnderstanding relationships between environmental characteristics and variation in species occurrence and density can provide information for managing human activities, protected species, and species of commercial importance in a dynamic system. To identify environmental drivers associated with variation in harbor seal (Phoca vitulina) densities in the Salish Sea, Washington, we analyzed 20 years of boat‐based survey data and environmental covariates using a hierarchical distance sampling model. We included spatial, temporal, and spatiotemporal environmental covariates in our model and produced fine‐scale predictive maps displaying in‐water estimated densities from our model results. We found that spatial covariates were the strongest predictors for harbor seal densities in the Salish Sea. Harbor seals were more abundant closer to major river mouths, near shore, in shallower waters, and in areas with more haul‐out sites. Additionally, harbor seal density varied with shoreline type. Changes in predicted harbor seal spatial use of the Salish Sea varied but with little difference between breeding/molting and nonbreeding/nonmolting seasons. Our results revealed spatiotemporal variation in harbor seal fine‐scale density in the Salish Sea, which are particularly important for conservation planning, as spatiotemporal variation in harbor seal density can exert heterogenous top‐down effects on prey species populations, some of which are threatened.