This study investigated the relationships between cetacean occurrence/relative density and environmental variables, and examined how these links vary both spatially and temporally. Data were collected during surveys carried out from passenger ferries throughout 2001 to 2006. The survey area covered three hydrographically distinct regions: the northern Minch, the Little Minch and the Sea of Hebrides. 17,649 km of survey effort was conducted in Beaufort sea-states 2 or less during which 990 sightings and 2,233 individuals were recorded. Six species of cetacean were recorded: the harbour porpoise, northern minke whale, short-beaked common dolphin, common bottlenose dolphin, white-beaked dolphin and Risso’s dolphin. Basking shark sightings were also recorded. The Minch had the highest diversity of cetacean species, with all six species sighted there. In the Sea of Hebrides, four species were recorded, and the Little Minch had the lowest diversity, with just three species. Relationships between harbour porpoise occurrence and environmental variables differed between months and regions. Minke whale presence was also linked to local environmental variables. However, while some relationships remained constant across all of the regions during specific times of the year, others were only evident in either the northern or southern areas. The habitat preferences of common dolphins and basking sharks in the Sea of Hebrides were found to be similar in some respects, despite their dietary differences. This may reflect the fact that both are pelagic predators. No significant relationships were identified between bottlenose dolphin occurrence and the environmental variables, which may be related to the large spatial scale of this study. These spatio-temporal variations in occurrence and habitat preferences may have important implications for any conservation measures or management strategies which may be applied to these regions, as it cannot be assumed that the Hebrides can be treated as a single homogenous area of habitat.