Maintaining soil functions is crucial for human well-being, but there is a lack of integration between soil, water security, ecosystem services, and climate change. To bridge this knowledge gap and address erosion-induced soil and water losses and considering intrinsic impacts of soil structure, a three-year-long study was conducted focused on three dominant soil types (Typic Hapludult, Typic Dystrudept, and Typic Usthortent) combined with different land uses (native forest, eucalyptus plantation, rotational grazing, and extensive grazing) in a critical water supply region for the São Paulo metropolitan area in Southeastern Brazil. Surface runoff, evaluated for erosion resistance, was measured using the Cornell infiltrometer, and soil electrical resistivity tomography estimated soil water content to a depth of 1.5 m for groundwater recharge analysis. Soil hydraulic properties were also measured. The results revealed that native forest soils had higher hydraulic conductivity, particularly in the surface layer, compared to eucalyptus and pastures. Native forests in Typic Hapludult showed a higher runoff rate (200 to 250 mm h−1) due to a naturally dense subsoil layer that negatively impacted water infiltration and recharge with a high erosion potential, therefore reducing the amount of water stored. Typic Usthortent maintained a higher soil water content in pastures than in other land uses and also showed a low rate of water infiltration, resulting in perched water in the surface layer. In Typic Dystrudept, the native forest presented higher hydraulic conductivity (0–5 cm: 115.9 cm h−1) than eucalyptus (0–5 cm: 36.4 cm h−1), rotational grazing (0–5 cm: 19.4 cm h−1), and extensive grazing (0–5 cm: 2.6 cm h−1), but there were no significant differences in soil water content among land uses. This work illustrates the crucial role of native forests in affecting deep water recharge, reducing the soil surface erosion, mainly in soils without naturally subsoil layer, maintaining recharge potential. For Ultisols, pastures preserved soil structure and are therefore less impacted by soil management. With these results, a contribution is made to soil and water conservation, providing support for sustainable management practices in erosion-prone areas.