Human activities increasingly affect cold-water specialists in mountain ecosystems, both through direct alteration of freshwater habitat and through indirect effects mediated by terrestrial ecosystem change. Using presence/absence data for three native and three non-native trout species in the Alberta Rocky Mountains, Canada, we model the change in occupancy probability across 20 years (2001 to 2020) in 74 watersheds and relate occupancy with habitat variables (i.e., elevation, tree coverage, and density of linear features). Native bull trout showed significant declines in HUC10 occupancy (-0.16 % year^-1) while non-native trout showed stability. Native trout favoured areas of higher elevation and greater tree coverage in direct contrast to non-native trout. Bull trout were significantly negatively impacted by the density of linear features. Our analysis suggests that regulation of anthropogenic activities and restoration of the terrestrial environment are required to conserve native trout in sensitive mountain environments.