Increasingly, baseline knowledge of habitat preferences and movement patterns of marine species is required to inform anthropogenic developments. The aim of this study was to determine baseline spatio-temporal distribution and habitat preference of cetaceans in the coastal waters of Algoa Bay. Areas of potential conflict with anthropogenic activities were also assessed. Monthly sea-based surveys were conducted between June 2008 and May 2011. A total of 500 cetacean sightings comprising six species were recorded in 106 surveys. Tursiops aduncus (Indo-Pacific bottlenose dolphin), Sousa plumbea (Indian Ocean humpback dolphin), Delphinus capensis (long-beaked common dolphin) and Balaenoptera brydei (Bryde's whale) were observed year-round, while Eubalaena australis (southern right whale) and Megaptera novaeangliae (humpback whale) were recorded from May to December. A large portion of sightings were associated with a Marine Protected Area and shipping zones. Eubalaena australis, T. aduncus and S. plumbea were found inshore (water depths < 12 m), while the other species were associated with deeper waters. Tursiops aduncus were most commonly seen (233 sightings). Megaptera novaeangliae were sighted often in austral winter, with 113 sightings. Only nine D. capensis sightings were recorded. Spatial distributions of species were corrected for search effort to identify habitat preferences. A number of key observations were made, including opportunistic foraging in M. novaeangliae, and the expansion of nursery grounds for E. australis, to include Algoa Bay. Four preferred habitat areas are proposed, providing important information for conservation and management of cetaceans in Algoa Bay. The spatial approach can be used to inform future relevant management decisions elsewhere.