<p>Rivers and wetlands are one of the most biologically diverse ecosystems facilitating vital habitats for a wide range of species. However, the species within these ecosystems are increasingly threatened by climate change and anthropogenic pressures. The black-bellied tern (<i>Sterna acuticauda</i>), an endangered riverine bird endemic to the Indian subcontinent, is highly reliant on wetland environments. Once widespread in South and Southeast Asia, the species is now locally extinct in much of Southeast Asia. Despite being recognized as a threatened and endangered species in Asia, no comprehensive climate-based assessment has yet been conducted. Accordingly, the present study was conceptualized to address these critical knowledge gaps by evaluating species responses to climatic change under both present and projected future conditions. This study evaluates the potential impacts of climate change on habitat suitability and corridor connectivity of <i>S. acuticauda</i> across the Ganges–Brahmaputra–Mahanadi (GBM) River Basin, which remains a key refuge, harboring over 90% of the global population. Current estimates indicate that only 5.09% of the GBM Basin presently provides suitable habitat for this species, which is projected to decline markedly under future climate change scenarios due to ongoing climatic shifts. Moreover, these declines are expected to lead to severe fragmentation of suitable habitats in the future. Circuit-based modeling identified five key ecological corridors, all of which are projected to experience connectivity loss. Hence, a regionally coordinated 10-year conservation and species-recovery program is strongly recommended, integrated with existing river basin initiatives and transboundary cooperation, to safeguard priority riverine habitats, regulate anthropogenic pressures and infrastructure development, strengthen community-based management, and implement comprehensive population monitoring to avert extinction of this critically imperiled species.</p>