Hydrological responses corresponding to the agricultural land use alterations are critical for planning crop management strategies, water resources management, and environmental evaluations. However, accurate estimation and evaluation of these hydrological responses are restricted by the limited availability of detailed crop classification in land use and land cover. An innovative approach using state-of-the-art Variable Infiltration Capacity (VIC) model is utilized by setting up the crop-specific vegetation parameterization and analyse the effect of uniform and heterogeneous agricultural land use over the hydrological responses of the basin, in the Kangsabati River Basin (KRB). Thirteen year simulations (1998–2010) based on two different scenarios i.e., single-crop in agricultural land use (SC-ALU) and multi-crop in agricultural land use (MC-ALU) patterns are incorporated in the model and calibrated (1998–2006) and validated (2007–2010) for the streamflow at Reservoir and Mohanpur in the KRB. The results demonstrated that the VIC model improved the estimates of hydrological components, especially surface runoff and evapotranspiration (ET) at daily and monthly timescales corresponding to MC-ALU than SC-ALU (NSC > 0.7). Grid-scale ET estimates are improved after incorporating heterogeneous agricultural land use (NSC > 0.55 and R 2  > 0.55) throughout the period of 1998–2010. This study improves our understanding on how the change in agricultural land use in the model settings alters the basin hydrological characteristics, and to provide model-based approaches for best management practices in irrigation scheduling, crop water requirement, and management strategies in the absence of flux towers, eddy covariance, and lysimeters in the basin.