The Atlantic surfclam, Spisula solidissima, and ocean quahog, Arctica islandica, are biomass dominant bivalve species on the eastern North American continental shelf, both supporting lucrative commercial fisheries in the Mid‐Atlantic with a combined value of about $53.6 million in ex‐vessel revenue per year. The thermal tolerance of Atlantic surfclam is generally below 20 °C, whereas the boreal ocean quahog resides in colder waters maintained by the Mid‐Atlantic Bight Cold Pool. Climate‐induced warming of bottom water temperatures is thought to be linked to the observed distributional shift of the Atlantic surfclam population into waters historically dominated by ocean quahogs. As climate change is expected to continue, this study investigated the future distributions of the two species from years 2016 to 2095 using projected bottom water temperatures and a temperature‐dependent population dynamics model. Simulations show the progressive colonization of Atlantic surfclams offshore into the region earlier occupied by the Cold Pool throughout the 79‐year projection, beginning between the mid‐2040s and mid‐2050s, effectively compressing ocean quahog habitat on all sides. Ocean quahogs are shown to be vulnerable to climate‐induced warming on both the southern, inshore, and offshore portions of the continental shelf, ultimately restricting their habitat by the end of the 21st century to the remaining core of the Cold Pool off Long Island. Atlantic surfclams, however, are likely to be less vulnerable to climate‐induced warming, ultimately increasing their geographic footprint across the MAB. Model projections indicate a large‐scale reorganization event of the continental shelf benthic community structure throughout the remainder of the 21st century.