The coral reef region of the Halmahera waters situated within the tropical area of the coral triangle, covers approximately 193,126 km2, with coral reef habitats occupying roughly 958.47 km2. The coral reefs in Halmahera waters are essential for ecosystem services and local fisheries. However, they are at risk from climate change and coastal pollution. This study aimed to develop habitat suitability models for coral reefs in the Halmahera waters under future climate change scenarios. MaxEnt modeling was employed to project suitability for the coral Acropora spp. using occurrence data. Suitability projections were made for 2050 under IPCC RCP 2.6, 6.0, and 8.5 scenarios, assuming no measures are taken to mitigate coastal water pollution. Environmental factors considered in the modeling included temperature, salinity, current velocity, pH, sunlight penetration, and chlorophyll levels. Results demonstrated a significant decline in habitat suitability, with an 85% loss of highly suitable areas under RCP 2.6 – 8.5 compared to current conditions (741 km2). Chlorophyll levels, a marker of coastal pollution, were predicted to be the most influential factor, followed by temperature and salinity. The findings highlight the need to reduce global carbon emissions and implement conservation measures to mitigate coastal water pollution in preserving coral reef habitats.