Climate change is altering marine ecosystems across the globe and is projected to do so for centuries to come. Marine conservation agencies can use short- and long-term projections of species-specific or ecosystem-level climate responses to inform marine conservation planning. Yet, integration of climate change adaptation, mitigation, and resilience into marine conservation planning is limited. We analysed future trajectories of climate change impacts on total consumer biomass and six key physical and biogeochemical drivers across the Northwest Atlantic Ocean to evaluate the consequences for Marine Protected Areas (MPAs) and Other Effective area-based Conservation Measures (OECMs) in Atlantic Canada. We identified climate change hotspots and refugia, where the environmental drivers are projected to change most or remain close to their current state, respectively, by mid- and end-century. We used standardized outputs from the Fisheries and Marine Ecosystem Model Intercomparison Project and the 6th Coupled Model Intercomparison Project. Our analysis revealed that, currently, no existing marine conservation areas in Atlantic Canada overlap with identified climate refugia. Most (75%) established MPAs and more than one-third (39%) of the established OECMs lie within cumulative climate hotspots. Our results provide important long-term context for adaptation and future-proofing spatial marine conservation planning in Canada and the Northwest Atlantic region.