Non-native lake trout, Salvelinus namaycush (Walbaum), threaten native salmonid populations in the western United States. Effective management of lake trout requires understanding movements within connected lake and river systems. This study determined the seasonal movements of subadult lake trout in the Flathead River upstream of Flathead Lake, Montana, USA using radio telemetry. The spatiotemporal distribution of lake trout in the river was related to water temperature. Lake trout were detected in the river primarily during autumn, winter and spring, when water temperatures were cool. By contrast, fewer were detected when temperatures were warmest during summer and during high spring flows. Downriver movements to Flathead Lake occurred throughout autumn and winter when water temperature decreased below 5 °C, and in late spring as water temperature rose towards 15 °C and river discharge declined following spring runoff. Upriver movements occurred primarily in October, which coincided with migrations of prey fishes. These results suggest that lake trout are capable of moving throughout connected river and lake systems (up to 230 km) and that warm water temperatures function as an impediment to occupancy of the river during summer. Controlling source populations and maintaining natural water temperatures may be effective management strategies for reducing the spread of non-native lake trout.