There have been marked declines of UK harbour seal populations over at least the last decade. Protected areas, such as Special Areas of Conservation (SACs), provide one tool to improve the conservation status of these populations. However, the design and management of SACs is often limited by a lack of information on long-term patterns in the use of seal haul-out sites and foraging areas. The Moray Firth is the only UK region where long-term harbour seal population studies have been conducted in parallel with detailed studies of foraging ecology. We used this opportunity to investigate changes in the use of haul-out sites and foraging areas within two adjacent estuaries, where annual haul-out counts were made over a 20-year period. In 1988, >99% of seals and all mother-pup pairs were located at haul-out sites within an area that was subsequently designated as a SAC to protect harbour seals. In addition to previously reported declines in this area, we detected a shift in haul-out distribution resulting from the development of a new pupping site that, by 2008, held 37% of mother pup pairs in the area. Foraging areas of breeding females were compared in 1989 and 2009 using a combination of VHF and GPS–GSM telemetry, confirming that females foraged in broadly similar areas in both periods. This suggests that the development of this new pupping site was not driven by the need to forage further offshore, but instead was more likely due to local variation in haul-out site characteristics. These results are discussed in relation to potential drivers of haul-out site choice and the need to develop a broader suite of measures for managing habitat quality within this and other SACs for harbour seals.