Marine protected areas (MPAs) are important conservation tools for safeguarding marine systems, yet they are increasingly impacted by climate change. Connectivity is a fundamental aspect of MPA design and evaluation, but regional patterns of marine ecological connectivity are often not well understood, nor how connectivity patterns may be affected by climate change. Our objective was to assess how ecological connectivity between MPAs may shift with projected ocean temperature changes in the Northern Shelf Bioregion in British Columbia, Canada, and demonstrate a potential approach that can be used in other systems. We conducted a case study with Dungeness Crab (Metacarcinus magister) and Shortspine Thornyhead (Sebastolobus alascanus) using benthic temperature outputs from a regional ocean model for hindcast (1981–2010) and future (2041–2070) periods coupled with species’ environmental preference information. We evaluated MPA exposure to projected temperature changes and suitability for the adult stage of the focal species. Using existing least-cost and circuit theory-based tools more often applied in terrestrial systems, we identified potential linkages between MPAs via adult movement, simulating both optimal and probabilistic paths, then compared MPA interconnectedness between time periods. There was a marked decrease in MPA suitability and interconnectedness for Shortspine Thornyhead under projected future climates, while there was a marked increase in MPA suitability for Dungeness Crab and minor increase in MPA interconnectedness. Given the contrasting results in connectivity changes when examining just two species, this study highlights the challenge of building climate resilience in MPA network designs with multispecies objectives.