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1. Information gaps resulting from incomplete data used to describe habitat configuration frequently hinder the efficacy of habitat protection action (HPA) for an animal with a wide distribution range. Such concerns are particularly important for the Indo-Pacific humpback dolphin, inhabiting disturbed coastal and estuarine habitats.2. This study inspected the likely habitat use of the Taiwanese humpback dolphin, an endemic subspecies that inhabits a highly disturbed habitat. Habitat use was evaluated using species distribution modelling with occurrence data from field surveys and remotely sensed oceanographic layers.3. Likely core habitats of the Taiwanese humpback dolphin were predicted near estuaries. The chlorophyll-a concentration was the primary factor affecting the distribution of the Taiwanese humpback dolphin. Bathymetry influenced the humpback dolphin distribution in the early 1980s, but became less important in the early 2010s. 4. Significant sea surface temperature increases in the estuarine and coastal waters and chlorophyll-a concentration decreases in the inshore waters were observed from the 1980s to the 2010s, indicating declining ecosystem productivity and shifting ecosystem functions. These oceanographic changes may be associated with adverse consequences of coastal alterations in western Taiwan. 5.We propose revising the current HPA scope by refining the HPA zoning, integrating coastal and watershed management, implementing regulatory fishery management, and designing and conducting restoration measures in compromised habitats and watershed landscapes.The need to reassess the current baselines of habitat use and HPA complex for the humpback dolphin across its natural range has been addressed.