The west coast of Scotland is comprised of complex coastlines and topography, and a range of physical processes influence its coastal marine environment. The region is host to one of the highest densities of harbour porpoise Phocoena phocoena in Europe. The aim of this study was to identify habitat preferences driving the distribution of harbour porpoise, to gain a better understanding of the spatial distribution of the species in the region, as well as to assess the consistency of such patterns across time and space. Visual and acoustic line-transect surveys were conducted between 2003 and 2010. Generalised Additive Models (GAMs) with Generalised Estimating Equations (GEEs) were used to robustly determine relationships between the relative density of harbour porpoises and temporally and spatially variable oceanographic covariates. Predictive models showed that depth, slope, spring tidal range and distance to land were consistently important in explaining porpoise distribution. Consistent preferences for water depths between 50 and 150 m and highly sloped regions were observed across the temporal models. Predicted distributions revealed a consistent inshore presence for the species throughout the west coast of Scotland and confirmed that predictable oceanographic features could help inform the establishment of Special Areas of Conservation (SACs) for the species.