Indonesia's only freshwater dolphin is the facultative Irrawaddy river dolphin Orcaella brevirostris in the Mahakam River in East Kalimantan, Borneo. To clarify the status of this Critically Endangered subpopulation we carried out a series of surveys from early 1999 until mid 2002 on abundance, habitat use, population dynamics and threats. Our estimates of total population size were 33–55 dolphins (95% confidence limits 31–76) based on direct counts, strip-transect analysis, and Petersen and Jolly-Seber mark-recapture analyses of photo-identified individuals. Mean minimum annual birth and mortality rates were similar, i.e. 13.6 and 11.4%, and no changes in abundance >8% were detected over 2.5 years. Dolphins died mainly from entanglement in gill-nets (73% of deaths). The dolphins' main habitat includes confluence areas between the main river and tributaries or lakes. Dolphins make intensive daily use of these confluences, moving up and downstream over an average length of 10 km of river and within a 1.1 km2 area. These areas are also important fishing grounds and subject to intensive motorized boat traffic. Sixty-four percent of deaths (1995–2001) with known location (n = 36) occurred in these areas. Interviews with local residents revealed a generally positive attitude towards the establishment of protected areas for this subpopulation. Because of the dolphins' dependence on areas that are also used intensively by people, primary conservation strategies should be to increase local awareness and introduce alternative fishing techniques.