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Abstract Interjurisdictional migrations lead to seasonally changing patterns of exploitation risk, emphasizing the importance of spatially explicit approaches to fishery management. Understanding how risk changes along a migration route supports time-area based fishery management, but quantifying risk can be complicated when multiple fishing methods are geographically segregated and when bycatch species are considered. Further, habitat selection in dynamic environments can influence migration behavior, interacting with other management objectives such as water quality and habitat restoration. As a case study, we examined a novel acoustic telemetry data set for Lake Whitefish in Lake Erie, where they migrate through multiple spatial management units that are variably affected by seasonal hypoxia and host a variety of fisheries. Combining telemetry results with fishery catch and water quality monitoring, we demonstrate three exploitation risk scenarios: (i) high risk due to high residency and high catch, (ii) high risk due to high residency in time-areas with moderate catch, and (iii) low risk due to residency in time-areas with low catch. Interestingly, occupation of low risk refugia was increased by the development of hypoxia in adjacent areas. Consequently, fishery management goals to sustainably manage other target species may be directly and indirectly linked to water quality management goals through Lake Whitefish.