Agricultural water drainage can significantly lower groundwater levels and affect catchment hydrology. Therefore, building models with and without these features can indicate an adverse impact on the geohydrological process. Therefore, the standalone Soil Water Assessment Tool (SWAT+) model was initially developed to simulate streamflow at the Kleine Nete catchment outlet. Next, a physically based and spatially distributed groundwater module (gwflow) was integrated into the SWAT+ model and calibrated for stream discharge at the catchment outlet. Finally, the same model was calibrated for both streamflow and groundwater heads. These final model parameters are used to investigate the basin-wide hydrologic fluxes with and without including agricultural drainage systems in the model scheme. The result suggested that the standalone SWAT+ model poorly represented the stream discharge and attained low NSE values of 0.18 and 0.37 during the calibration and validation periods, respectively. Integrating the gwflow module to SWAT+ improved the model representation of stream discharge (NSE = 0.91 and 0.65 for calibration and validation periods, respectively) and groundwater heads. However, calibrating the model for only streamflow resulted in a high root mean square error (above 1 m) for groundwater head, and the seasonality is not captured. On the other hand, calibrating the coupled model for streamflow and hydraulic head reduced the root mean square error (below 0.5 m) and captured the seasonality of groundwater level fluctuations. Finally, drainage application resulted in a 50 % (from 33.04 mm to 16.59 mm) reduction in groundwater saturation excess flow and an 18.4 mm increment in drainage water to streams. To conclude, the new SWAT+gwflow model is more appropriate than the standalone SWAT+ model for the case study. Furthermore, calibrating the SWAT+gwflow model for streamflow and groundwater head has improved the model simulation, with implications for general coupled models where representing surface and groundwater in ...