Climate change is exerting significant pressure on hydrology and water resources, leading to increased variability in hydrological regimes and water availability in various regions around the world. This study focuses on two politically distinct but interconnected geographical areas, Northeast India (NEI) and Bangladesh, to conduct a comprehensive analysis of the consequences of climate change on water systems. This article reports our recent findings on the variations in temperature and precipitation-based indices across the Northeast India-Bangladesh region, including West Bengal (NEIB). There is a substantial temperature increase, reaching up to 4–5.5 °C by the end of the twenty-first century under the SSP585 scenario. Warm spell days are projected to increase by approximately 2 days, and the Simple Daily Intensity Index (SDII) is expected to rise from 14.4 mm/day to 16.8 mm/day. We further consider a river basin, namely the Gomati River basin, situated in Tripura, one of the Indian states in the Northeast, where rising temperatures have caused increased evapotranspiration rates and declining river flow. The analysis also underscores the significance of reducing the streamflow of the Gomati River basin, which can range from 12 to 30% under varying scenarios. Projections suggest that these trends will intensify in the coming years, potentially leading to water shortages for agriculture and urban areas across the NEI. By understanding the diverse regional vulnerabilities to climate change, we aim to facilitate the development of adaptive strategies, collaborative agreements, and policies that can mitigate the adverse effects on hydrology and water resources in these vital areas.