Understanding the movement ecology of fish communities is necessary to take effective management actions that aim to reverse population declines, especially in fish stocks containing sympatric subpopulations with local adaptations, such as Northern pike (Esox lucius) in the Baltic Sea. We followed the movement and survival of adult pike for one year by tagging 198 individuals in an estuary (an anadromous subpopulation) as well as in two neighbouring bays (individuals of unknown origin) with acoustic transmitters. We found that the estuary was vital in sustaining the local coastal pike stock, that anadromous pike mainly inhabited a coastal area with a radius of 3 km and aggregated in large numbers in the estuary several months prior to spawning. Management should thus prioritise to identify, restore, and protect estuaries from exploitation. The two neighbouring bays demonstrated distinct differences in spatiotemporal aggregations of pike with no aggregations prior to, and during, spawning in the bay without estuaries. The habitat choice during spawning season suggests that 92% of pike sampled in the bay adjacent to the estuary belong to the anadromous subpopulation, while 94% of pike sampled in the neighbouring bay belong to unknown subpopulation(s) of resident brackish spawners. Survival of tagged pike was 84% and suggest low mortality from fisheries and top predators, which have been proposed as threats to pike populations in other areas of the Baltic Sea. Together, these results call for management of high resolution and highlight the importance of detailed movement data.