The Deduru Oya Basin (DOB) is the sixth-largest river basin in Sri Lanka, and it faces significant flooding during the monsoon season and prolonged droughts during dry periods, making accurate forecasting of future river flow essential for effective water resource management and hydraulic structure design. To assess future river flow in the DOB, a rainfall–runoff model was developed, integrating HEC-HMS for basin routing and HEC-ResSim for reservoir simulation, calibrated against observed data. The integrated model was simulated using bias-corrected future rainfall data derived from the CNRM-CM6-1 Global Climate Model, across two carbon emission scenarios (SSP2-4.5 and SSP5-8.5) and three timeframes: Near Future (2025–2040), Middle Future (2041–2070), and Far Future (2071–2100). The implications of climate change on river flow were assessed through box plot comparisons, General Extreme Value analysis for flood events, and Flow Duration Curve (FDC) analysis within the three timeframes and two SSPs. Projections suggest that the DOB may experience modest increases in flow, ranging from 4% to 12% for the two SSPs. However, our analysis indicates that historical 50-year flood events could occur every 25 years under an extreme climate scenario. Furthermore, the FDC analysis reveals a significant decline in base flow under both scenarios, which is likely to be exacerbated during drought conditions. This decline could have detrimental effects on agricultural sustainability and groundwater recharge. These findings underscore the urgent need to improve flood and drought preparedness in the future.