Groundwater recharge in sedimentary basins is often assumed to be locally controlled, yet increasing evidence suggests the importance of spatially distributed and multi-scale processes. Here, we investigate the controls on groundwater recharge in the Taubaté Sedimentary Basin (southeastern Brazil) using stable isotopes (δ¹⁸O and δ²H), d-excess, and electrical conductivity data from precipitation, springs, and deep wells. Results reveal a clear decoupling between local precipitation and deep groundwater recharge. Most groundwater samples plot below the Local Meteoric Water Line (LMWL) and exhibit reduced regression slopes, indicating the influence of mixing, delayed percolation, and non-conservative recharge processes. Deep groundwater shows low isotopic variability and weak seasonal signals, consistent with longer residence times and regional flow integration. In contrast, spring waters display greater variability and stronger sensitivity to seasonal inputs and near-surface processes. A closer isotopic correspondence between deep groundwater and precipitation from higher-altitude areas suggests that effective recharge occurs preferentially in elevated zones and is subsequently redistributed toward lower basin sectors. Electrical conductivity and d-excess relationships further indicate that shallow groundwater is influenced by evaporation and short flow paths. Together, these findings support a conceptual model of a dual groundwater system, characterized by the coexistence of rapid, shallow flow paths and slower, regionally integrated deep circulation. This study highlights the importance of spatially decoupled recharge and cross-scale groundwater dynamics for understanding hydrological functioning in sedimentary basins.