Coastal and estuarine waters are important ecosystems with high primary and secondary productivity, but they are prone to the impacts of habitat loss caused by anthropogenic activities. For species exclusively inhabiting coastal and estuarine waters, such as the Indo‐Pacific humpback dolphin, Sousa chinensis, irreversible habitat loss can have dramatic implications for population viability. A Landsat image database was used to determine the extent of coastal changes along the northern Beibu Gulf, where a large humpback dolphin population is found. The results were compared with the standardized sighting gradient (SPUF) determined from a questionnaire survey of fishermen and likely core habitats identified by application of a global digital elevation model. Both SPUF and likely core habitat results indicated a continuous distribution of the humpback dolphin along the northern Beibu Gulf. Landsat images revealed that 129.6 km2 of coastal waters were permanently lost in the past 40 years, 60 km2 within the likely core habitats. Although this may be considered small, the impact of such habitat loss could be substantial in some local habitats. The humpback dolphin population in the northern Beibu Gulf should be regarded as one management unit, with two or more social subunits. Immediate systematic surveys are needed to fill information gaps on true distribution range and habitat‐use patterns. Habitat protection actions for dolphins in the northern Beibu Gulf should include both core and linking habitats, including enacting protected areas in core habitats, mitigating anthropogenic impacts in likely habitats, restoring both coastal waters and surrounding landscape quality, effective treatment of industrial sewage discharge, and comprehensive environmental impact assessments for the planning of coastal development projects.