Marine ecosystems across the globe are under pressure requiring evaluations of whether marine protected areas (MPAs) remain effective in safeguarding marine life and critical habitats. Our objectives were to 1) estimate shifts in seasonal habitat suitability over a 25-year period (1997–2022) for the harbour porpoise (Phocoena phocoena) across the North Sea–Baltic Sea transition zone, and 2) quantify any spatiotemporal changes in the overlap between suitable habitats and an existing network of 62 MPAs (an area covering 16,404 km2) dedicated to harbour porpoise protection. Habitat suitability was estimated using the maximum entropy (MaxEnt) algorithm, based on satellite tag data of 111 individuals and a range of dynamic and static environmental conditions as predictor variables. Model output revealed a northward shift of medium and high suitable habitats during winter (Nov–Apr) over the study period. Changes in habitat suitability during summer (May–Oct) were also evident though without clear directional shifts. A maximum of 14.5 % of the MPAs (n = 9; area of 1096 km2) were found to overlap with highly suitable habitat during the summers of 2005–2012, with a minimum of 6.4 % (n = 4 MPAs; area of 194 km2) during the winters of 2013–2022. These results clearly indicate a decline in the spatiotemporal overlap between habitat suitability during winter and the location of MPAs dedicated to harbour porpoise protection in the North Sea–Baltic Sea transition zone. The model output may inform effective design of forthcoming MPAs under the EU Biodiversity Strategy for 2030.