Climate change impact on flow regimes in the Gomti River basin, India was studied using the Soil Water Assessment Tool (SWAT) driven by climate change scenarios generated from multiple general circulation model (GCM) projections. The SWAT-CUP (SWAT-Calibration and Uncertainty Programs) was used for calibration and validation of SWAT using multi-site data. Climate change scenarios were generated from multiple GCM projections using the hybrid-delta ensemble method. Calibration of SWAT using the nine most sensitive parameters showed that the model performed reasonably well with P-factor >0.7 and R-factor <1.0. The annual rainfall is projected to increase by 3.4–4.5, 4.7–10.0, and 5.0–18.0% during the 2020s, 2050s, and 2080s respectively under different Representative Concentration Pathways (RCPs). There is a decrease in rainfall during the winter season. The annual streamflow is projected to increase by 1–9, 1–22, and 2–38% during the 2020s, 2050s, and 2080s, respectively. However, winter and summer streamflow is projected to decrease. Magnitude and frequency of high flows is also projected to increase in the range of 3.6–27.3 and 12–87%, respectively under different RCPs. The results of this study will be helpful in developing suitable water management adaptation plans for the study basin.