The harbour porpoise is a highly mobile species and thus represents a considerable challenge in the context of using marine protected areas (MPAs) for conservation. The shelf waters off the west coast of Scotland have been identified as an area of year-round presence, high density in comparison to surrounding areas, and a high young to adult ratio in summer and are thus a suitable area for exploring the location of possible special areas of conservations (SACs) under the EU Habitats Directive. We carried out dedicated surveys over three summers in the southern Inner Hebrides and used generalised additive models (GAMs) to predict areas of high relative density for harbour porpoises for each year. After compensating for survey effects, static bathymetric and persistent hydrographic variables were used in a step-wise model selection procedure. In all years harbour porpoise distribution was best explained by maximum tidal current, with higher densities predicted in areas of low current, and the same high density areas predicted year-on-year. Perimeter-to-area ratio was used to identify which areas should be considered as a basis for designating SACs for harbour porpoise in this area, to form part of the Natura 2000 network. The method used here combines spatial modelling and perimeter-to-area ratio for selecting protected areas, a methodology which is suitable for the protection of other animal species.