The current study analyses the effect of root zone soil moisture in the calibration and validation of Soil and Water Assessment Tool (SWAT) model. A multi-algorithm, genetically adaptive multi-objective method (AMALGAM) is used for the calibration of the model. The multi-variable calibration considering both streamflow and soil moisture is compared with a single-variable calibration considering streamflow and then analysed the effectiveness of root zone soil moisture in the calibration of SWAT. The results of the analysis show that the root zone soil moisture significantly influences the simulation of evapotranspiration component in SWAT. The SOL_AWC and SOL_K are found to be the key parameters for the simulation of hydrological fluxes in SWAT. The multi-variable calibration at the watershed outlet ensures a better process representation and spatial prediction in SWAT compared to the single-variable calibration approach. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.