Cetacean living coastal habitat often suffer from anthropogenic disturbance, which would change their original distribution and core habitat use. Pearl River Estuary-Moyang River Estuary (PRE-MRE) population is the largest known (putative) population of Indo-Pacific humpback dolphin in the world. Lingding Bay is a critical habitat of PRE-MRE population, where human activities have become frequently in recent years and dolphin survival pressure is increasing. Analysis the response of Indo-Pacific humpback dolphin to environment change and making corresponding conservation strategy are urgent. This research mainly discussed coastal waters loss process in the past 43 years from sea reclamation in the Lingding Bay using the multi-source Landsat imageries. To examine the change of distribution and core habitat of dolphins, a new kernel density estimation approach that accounted for physical barriers to movements was applied with sighting records from line-transect surveys during past 20 years. Our results showed that about 344.08 km² waters became unavailable from 1986 to 2015; average proximity of sighting sites to artificial shoreline was farther than to natural shoreline and average proximity of sighting sites to artificial shoreline and natural shoreline decreased, which indicated that dolphin habitat use changed and dolphin had to adapt anthropogenic disturbance; habitat use of dolphin focused on eastern Lingding Bay waters and distribution range reached peak in 2005-2006, but fell sharply in 2015-2016; dolphin's core habitat approaching main channels and around undeveloped islands might be the only option result from resource depletion. The proportion of core habitat showed a decreasing trend in the Chinese White Dolphin National Nature Reserve of Guangdong Pearl River Estuary, which decreased from 79.9% to 49.4% in different period. We recommend that the government should adjust current protected range to fulfill the change pattern from habitat use.