The Indo-Pacific humpback dolphin (Sousa chinensis) is a small odontocete species that is widely distributed throughout inshore waters of the Indian and western Pacific oceans. This species is currently classified as "Near Threatened" by the IUCN in its red list of threatened species. The effective conservation of this species requires an understanding of the relationship between its populations and their habitats. The Pearl River Estuary contains one of the world's largest-known populations of this dolphin species; however, commercial development is extensively modifying the surrounding environment. Moreover, the region is densely populated, and the intensity of human activities, such as shipping and reclamation, are all increasing. The habitat of the Indo-Pacific humpback dolphin throughout the Pearl River Estuary is changing and life for the dolphins within it is becoming more complex. We used data collected during vessel-based line-transect surveys in 2012, augmented by data from nekton sampling by bottom trawls and environmental variables, to identify relationships between the environment and the distribution of S. chinensis in the western Pearl River Estuary. A total of 200 nekton species belonging to 81 families and 19 orders were collected during the four surveys. On the basis of humpback dolphin encounter rates, generalized additive models (GAM) were used to assess the relationships between dolphin encounters and nine environmental variables:Beaufort Sea state, depth, bottom water temperature, salinity, pH, dissolved oxygen, nekton density, prey species density, and distance to the shore. Nekton density, depth, prey species density, distance to the shore, and bottom water temperature were all significantly associated with dolphin encounter rate, and collectively explained 64.7% of the observed variance. GAM models revealed the habitat preferences of these dolphins. Along with an increase in nekton density, dolphin encounter rate fluctuated, initially increasing and then decreasing and increasing again. The reason for this observed pattern may be the proportion of dolphin prey in the nekton, indicating that prey density was not positively correlated with nekton density. Humpback dolphin distribution and prey density were closely related, although any effect of prey density decreased above a threshold level, suggesting that foraging time decreases in times of prey abundance. Water depth is considered to be a factor limiting the offshore distribution of humpback dolphins. We noted that humpback dolphins were more frequently observed in water depths of 10m, and this preference shown by dolphins for a certain water depth is the same as that recorded in other survey years. We also identified a relationship between dolphin encounter rates and bottom water temperature, with the encounter rates decreasing markedly when the bottom water temperature exceeded 19.5℃. It is likely that bottom temperature affects the distribution of prey species, which in turn influences the nature of dolphin distribution. Offshore distance is also an important factor determining dolphin distribution. With an increase in the offshore distance from 0.1 to 3km, the dolphin encounter rate increased monotonically with increasing distance. Thereafter, the encounter rate decreased monotonically when the offshore distance exceeded 3km. Because the preferred habitat of humpback dolphins occurs at a distance of less than 3km offshore, prioritized conservation of this environment would better protect and improve management of this increasingly threatened dolphin species.