Groundwater recharge is a key hydrological process for integrated water resource management, as it recharges aquifers and maintains the baseflow of perennial rivers. In Brazil, the Cerrado biome is an important continental recharge zone, but information on rates and spatial distribution is still lacking for this country. The objective of this work was to characterize the groundwater recharge process in phreatic aquifers of the Cerrado biome. For this, an experimental watershed representative of the referred biome was established and intensively monitored. The methodology consisted of an inverse numerical modeling approach of the saturated zone and three classic methods of recharge evaluation—hydrological modeling, baseflow separation, and water table elevation. The results indicated average potential recharge around 35% of the annual precipitation, average effective recharge around 21%, and higher rates occurring in flat areas of Ferralsols covered with natural vegetation of the Cerrado biome. As the level of uncertainty inferred from the methods was high, these results were considered a first attempt and will be better evaluated by comparison with other methods not applied in this work, such as the lysimeter and chemical tracer methods.