Marine Protected Areas (MPAs) are conservation tools that promote biodiversity by regulating human impacts. However, because MPAs are fixed in space and, by design, difficult to change, climate change may challenge their long-term effectiveness. It is therefore imperative to consider anticipated ecological changes in their design. We predict the time of emergence (ToE: year when temperatures will exceed a species’ tolerance) of 30 fish and invertebrate species in the Scotian Shelf-Bay of Fundy draft network of conservation areas based on climate projections under two contrasting emission scenarios (RCP 2.6 and RCP 8.5). We demonstrate a strong Southwest-to-Northeast gradient of change under both scenarios. Cold water-associated species had earlier ToEs, particularly in southwesterly areas. Under low emissions, 20.0% of habitat and 12.6% of species emerged from the network as a whole by 2100. Under high emissions, 51% of habitat and 42% of species emerged. These impacts are expected within the next 30–50 years in some southwestern areas. The magnitude and velocity of change will be tempered by reduced emissions. Our identification of high- and low-risk areas for species of direct and indirect conservation interest can support decisions regarding site and network design (and designation scheduling), promoting climate resilience.