Abstract The present study developed an integrated hydrologic model for sustainable utilisation and water management in two complex watersheds with varying physioclimatic features and reservoirs. The soil and water assessment tool (SWAT) is used for predicting integrated inflows into the Hatnur reservoir from the Burhanpur and Purna watersheds of the Upper Tapi River basin, while outflows are simulated using a rule curve. The influence of watershed complexities on hydrological model parameters and the watershed processes are investigated using extensive multisite and multivariable calibration (1998–2007) and validation (2008–2013) approaches, including sensitivity and uncertainty analyses. The sensitive parameters are related to curve number (CN), groundwater, slope, and main channel characteristics. The annual streamflow (m3/km2/mm of rainfall) in the Burhanpur watershed is 568.7, which is 4.2 times higher than the Purna watershed's streamflow of 136.2. The hypsometric analysis, areal rainfall, and flow duration curves revealed a substantially different streamflow pattern and a larger coefficient of variation in the spatial distribution of water balance components over sub-watersheds in the Burhanpur watershed compared to the Purna watershed due to diverse topographic features. The developed model would be useful for planning controlled releases from the terminal reservoir to mitigate hazards in the downstream reaches of the Tapi River basin.