Management of marine species has increasingly focused on key site protection. Initiatives to protect bottlenose dolphins, Tursiops truncatus, under the EU Habitats Directive reflect this trend. The boundaries of the Moray Firth candidate Special Area of Conservation (cSAC) were intended to include the main Scottish population's core range, following research conducted in the 1980s and early 1990s. However, during implementation, anecdotal sightings increased outside the cSAC. Here, the authors examine existing datasets to identify whether these reports reflect simply elevated awareness among public observers or real changes in distribution. Dolphins photo-identified in areas originally considered to be outside the population's range confirmed they originated from the protected population. These individuals became rarer within the cSAC during the 1990s. Scottish bottlenose dolphins kill harbour porpoises, Phocoena phocoena, and carcasses from these interactions also became more frequent outside the cSAC during the 1990s. These results indicate mobility of this ‘resident’ dolphin population on a timescale similar to that of the implementation of the European Directive designed to protect it. Consequently, this and other similar designations, may afford less protection than originally envisioned and the authors recommend, therefore, that the potential for long-term mobility should be actively incorporated into such management structures from the outset.