The population of Irrawaddy dolphins in Brunei Bay, Malaysia is currently under threat by anthropogenic activities. This study is aimed at contributing information on population size, group composition, spatial occurrence and habitat preferences of this dolphin species in the bay area. A total of 36 individuals (adults) of Irrawaddy dolphins were identified using dorsal fin photo match software (DARWIN) by undertaking 297.91 h of boat-based dedicated surveys (April 2013 – October 2015). By using the mark–recapture open-population parameterization, the estimated population size (adult) was 33 (95% CI = 28–39) with the apparent survival rate of 0.98 (0.89–0.99, SE = 0.01). Also, the recapture rate was 0.27 (0.14–0.45, SE = 0.07) and the estimated individual entry rate from super-population was 0.15 (0.10–0.22, SE = 0.03). The estimated entire population size was 41 (95% CI = 36–49) including calves. The observed mean group size was 6 (SE = 0.66, range 1–18). Two hotspots were identified for dolphin occurrences near Lawas and Labuan Island at a sighting rate of 2.8–12.3 km^-2. The dolphins were encountered in the bay over the entire year with no seasonal differences. The observation of dolphin calves in the groups are a positive indicator that the dolphins are breeding successfully in the Bay area and provide hope that the population will remain stable or increase in number. The dolphins showed habitat preferences of sea depths (2 to 9.99 m), surface water temperature (29 to 31.99°C), and coastline distance (1.5 to 4.49 km). This study provides the first detailed information about Irrawaddy dolphins in the Brunei Bay, Malaysia, and may serve as a baseline for future comparisons. It can help researchers, conservationists, local marine park managers and policy makers to propose effective conservation and management plans in the Brunei Bay area.