In humid subtropical regions, baseflow is mainly governed by aquifer discharges and this dynamic is fed by groundwater recharge. To better comprehend the watershed groundwater recharge using a large-scale approach, two watersheds located over the Serra Geral Aquifer System (Southern South America) were studied. Three different groundwater recharge methods were utilized to study the baseflow: a simplified water budget, a hydrograph separation using the Eckhardt filter with different ways of obtaining the BFI_max parameter, and the MGB–IPH hydrological model, which is unprecedented in being used for this purpose. These methods showed a general mutual convergence, where recharge magnitude remained similar in most methods. The MGB–IPH model proved to be a useful tool for understanding the occurrence of groundwater recharge. Uncertainties associated with the representativity of interflow demonstrated by hydrograph separation and shown in the model may indicate that the groundwater recharge estimate could be lower than those obtained considering hydrograph numerical filters.