Between June 2008 and September 2009, 56 days of small boat surveys were conducted off the coast of Sarawak, Malaysia with the aim of recording cetacean distribution. These surveys, which focused on the Miri, Bintulu-Similajau and Kuching regions, comprised 173 hours of survey effort and covered 2851 km of pre-determined systematic tracks. Surveys were clustered into three sets of seasonal snapshots: June-July, September-October and March-April. A total of 115 cetacean sightings were made, of which 65 were on-effort and used in analyses of cetacean encounter rates in relation to habitat characteristics. Species observed included (in order of frequency) Irrawaddy dolphins (Orcaella brevirostris), finless porpoises (Neophocaena phocaenoides), Indo-Pacific bottlenose dolphins (Tursiops aduncus) and Indo-Pacific humpback dolphins (Sousa chinensis). One hundred and ten of 115 sightings were made in less than 10 m water depth, highlighting the importance of nearshore coastal habitats for these species. Despite an apparent overlap in habitat, Irrawaddy dolphins showed a statistically significant affiliation with areas of shallower depth and closer proximity to shore and river mouths than finless porpoises or bottlenose dolphins. This preference for nearshore areas renders the species vulnerable to threats such as fisheries by-catch and habitat degradation from coastal development. Irrawaddy dolphins were more frequently encountered in Kuching, while the highest encounter rate for finless porpoises was in the Bintulu-Similajau region. The highest encounter rates in both Kuching and Similajau occurred in areas that are destined for major coastal developments.