Climate change is known to have a range of impacts on the marine environment, including the continuous variation of the distribution of species, and can cause significant challenges in planning conservation measures. This study focuses on the current and future habitat suitability of the striped dolphin (Stenella coeruleoalba), the common bottlenose dolphin (Tursiops truncatus) and the fin whale (Balaenoptera physalus) in the Mediterranean Sea. We integrated data collected in the Mediterranean Sea between 2009 and 2021 from official National and International research programs with public datasets and considered Earth Observation variables from the Copernicus Programme. We applied an ensemble of Species Distribution Models to predict their current and future potential distribution at the Mediterranean subregional scale under two climate change scenarios in the 2045–2055 period. Results suggest a reduction in suitable habitat for the three species. The fin whale and the bottlenose dolphin would be forced outside large portions of their current range and would have to deal with new conditions outside their ‘range of tolerance’. For the striped dolphin, the loss of a portion of suitable habitat would be compensated by the potential colonization of new suitable areas. This work draws attention to the dynamism of species distribution under shifting climatic conditions, a usually underestimated aspect, and highlights the importance of potential future patterns of species distribution in addressing the MSFD D1C4 and D1C5 criteria. This will support decision‐makers in planning long‐term sustainable management of European Seas.