The aquatic ecosystems are an integral part of the global environment and play a critical role in hydrogeological processes in the rivers. In recent decades, the external stressors on the aquatic species have significantly increased due to hydrologic alterations, human activities, and anthropogenic changes to their natural habitat. Global climate change has led to rivers' hydrological flow regime shifts, leading to unsuitable habitat conditions. It is, therefore, crucial to assess the potential implications of climate change on habitat suitability to ensure the long-term sustainability of freshwater species. In this direction, we investigated the association between endangered Gangetic dolphin populations and climate-driven hydrologic flow regime alterations in the Kulsi river, India. We developed a coupled eco-hydraulic framework comprising hydrological and hydrodynamic modeling to study the impact of past and projected climate change scenarios on the habitat suitability of target species. The framework was tested on a 15-km stretch of the Kulsi River, where the dolphin population has significantly declined in recent years. The temporal changes in the Weighted Usable Area (WUA) were analyzed using flow parameters and habitat suitability curves. Our findings suggest that the dolphin population decline coincided with a decrease in WUA, indicating a strong association between flow regimes and habitat suitability. Under climate change scenarios, multi-model climate projections and hydrological-hydrodynamic simulations show a rising trend in precipitation and streamflow in the basin, with substantial uncertainty. Higher flow depth and velocity would enhance WUA (habitat suitability). Still, the proposed river development projects in upstream regions could pose a serious threat to fragile dolphin communities by changing the seasonal flow patterns. The findings of this study can be included in conservation action plans and flow regulations strategies in upstream projects to ensure the long-term survival of endangered species.