The Irrawaddy dolphins in Guimaras Strait compose the second population to be reported in the Philippines. Their very small population size, isolation, and high vulnerability to human-induced threats in the coastal areas have earned them a local conservation status of critically endangered. Appropriate conservation and management of this species will need a better understanding of their relationship with their known habitat and interactions with human activities. Regular boat-based surveys were conducted in a defined study area in the coastal waters of Bago and Pulupandan, Negros Occidental, Philippines, to document behaviour and gather photo ID data from 2010 to 2016. Behaviour and habitat use were quantified using area use and activity indices, while site fidelity was analysed using photo catalogues. Of the nineteen catalogued individuals, at least eight dolphins were present throughout the study, indicating high site fidelity. The dolphins used a relatively small nearshore area spanning a commercial port and northward towards the mouth of Bago River. The Minimum Convex Polygon area is estimated at 12.68 km2 and is one of the smallest core areas known to have been recorded for this species. The dolphins showed a preference for areas with a steep increase in water depth and were often observed foraging, highlighting the importance of these areas as feeding grounds. Several threats to the dolphins were identified, most of which are related to human activities. Identifying the behavioural aspects of the Irrawaddy dolphins’ local ecology helps put the scope and limitations of managing their population into perspective and provides the critical information needed to delineate special management or conservation areas in their habitat.