In the second phase of the Distributed Model Intercomparison Project (DMIP2), the WetSpa model is applied to simulate flows at basin and subbasin scales. Parent basins and their nested subbasins are modeled as gaged and ungaged basins, respectively. Available observations in the subbasins were only used to validate the model predictions. Gaged basins simulation results show that the predictions and observations are in good agreement. However, major peaks are underestimated, as is often the case in runoff modeling. Underestimation of high flows and in particular peak flows indicates that the prediction of actual runoff coefficients in the current WetSpa model needs to be improved. Also, sensitivity analysis of the model parameters reveals that the baseflow recession coefficient is the most sensitive parameter and care should be taken when modeling ungaged basins. Hence, by estimating this parameter for each subbasin separately, the model performance for the subbasins can be improved. To do this, a Boussinesq groundwater flow equation is used to improve the prediction of baseflow recession coefficients in the subbasins. Comparison between the original and the modified WetSpa models shows that the modified model yields relatively higher performances for the subbasins, creating a more accurate model for predicting ungaged subbasins.