Abstract Globally, small‐scale inshore fisheries are being recognized as highly beneficial for underdeveloped coastal communities since they directly contribute to local economies. Community coastal fisheries, however, may target species that are simultaneously harvested by large commercial vessels in adjacent offshore waters, creating uncertainty over stock units and connectivity that complicate management. Greenland halibut Reinhardtius hippoglossoides, a commercially important flatfish species in the Arctic, were tagged in Scott Inlet, coastal Baffin Island, Canada, with acoustic transmitters and tracked for a 1‐year period. Our aim was to measure fish movement and connectivity between inshore habitats, where Inuit fisheries are developing, and offshore waters, where an established commercial fishery operates. Four movement metrics were established, and cluster analysis and a mixed effects model were used to define movement types and identify environmental covariates of the presence/absence within the coastal environment respectively. Two distinct movement patterns were characterized for Greenland halibut; the majority were transients that were no longer detected inshore by the end of November (n = 47, 72%), and a smaller group of intermittently resident fish that moved into the offshore at the same time as transient fish, but returned to the coastal environment in the winter (n = 8, 12%), with the remainder being undefined. The presence of Greenland halibut in the inshore was negatively correlated with ice cover, indicating that fish moved offshore as sea ice formed. Synthesis and applications. Greenland halibut were previously thought to be highly resident within the coastal environment of Baffin Bay; however, our data demonstrates that this is not true for all areas. In Scott Inlet and adjacent coastal regions, Greenland halibut exhibit complex inshore‐offshore connectivity, suggesting inshore and offshore fisheries require a shared quota. We recommend that in the face of developing global small‐scale coastal fisheries, improved understanding of stock connectivity between environments is required to sustainably manage commercial fish species.