Indo-Pacific humpback dolphins Sousa chinensis in Hong Kong (HK) waters are part of a large (ca. 2000-2500), but declining, population that occurs in the Pearl River Estuary of southern China. To understand the factors that may influence dolphin densities in 4 different parts of HK, a 25 yr (1996-2020) database containing 66439 km of line-transect survey effort and 4052 dolphin sightings was used. Seventeen variables representing natural and anthropogenic habitat factors were evaluated using generalized additive models (GAMs) to identify the preferred habitat of humpback dolphins in HK waters. In the environmental GAMs, rainfall, salinity, and river discharge were significant factors related to dolphin density, consistent with their observed strong preference for estuarine habitat. Sea surface temperature was also important for one of the 4 subareas. In the anthropogenic GAMs, the only significant variable was the amount of habitat area lost to land reclamation in North Lantau. This finding is consistent with previous hypotheses that heavy coastal engineering in North Lantau has contributed to observed declines in dolphin abundance during the study period. This study provides some of the first quantitative indications of factors that are potentially influencing the density of the animals in various parts of HK. As such, it will be a valuable tool for evaluating and mitigating potential impacts of both natural and anthropogenic factors on the population in the future.