Efforts to conserve endangered species usually involve attempts to define and manage threats at the appropriate scale of population processes. In some species that scale is localized; in others, dispersal and migration link demic units within larger metapopulations. Current conservation strategies for endangered shortnose sturgeon (Acipenser brevirostrum) assume the species is river resident, with little to no movement between rivers. However we have found that shortnose sturgeon travel more than 130 km through coastal waters between the largest rivers in Maine. Indeed, acoustic telemetry shows that shortnose sturgeon enter six out of the seven acoustically monitored rivers we have monitored, with over 70% of tagged individuals undertaking coastal migrations between river systems. Four migration patterns were identified for shortnose sturgeon inhabiting the Penobscot River, Maine: river resident (28%), spring coastal emigrant (24%), fall coastal emigrant (33%), and summer coastal emigrant (15%). No shortnose sturgeon classified as maturing female exhibited a resident pattern, indicating differential migration. Traditional river-specific assessment and management of shortnose sturgeon could be better characterized using a broader metapopulation scale, at least in the Gulf of Maine, that accounts for diverse migratory strategies and the importance of migratory corridors as critical habitat.