This study examines the hydrogeochemical processes shaping groundwater quality in the Ilhas-São Sebastião aquifer system, situated at the interface of the Central and Southern Recôncavo basins in the densely populated area near the Brazilian metropolis Salvador. Analysis of 71 groundwater samples reveals distinctive hydrogeochemical compositions in aquifers. In the São Sebastião aquifer, alkalis (Na+ + K+) and strong acids (Cl− and SO42−) prevail. Furthermore, a moderate correlation of Na+–Cl-marks an evolution from Mg–Ca–HCO3 to Mg–Ca–Cl and Na–Cl facies. In contrast, the Ilhas aquifer displays a Na+>Ca2+>Mg2+>K+ relationship for cations and HCO3− > Cl− > SO42− > CO32− for anions and a recharge-discharge trajectory from the Mg–Ca–HCO3 to the Ca–Na–HCO3 facies. Additionally, it presents greater mineralization and dispersion of physicochemical parameters, especially around sub-basin depocenters. Its hydrogeochemical signature is characterized by robust correlations between TDS and EC, and between these parameters and SO42−, HCO3−, Ca2+, and Mg2+, complemented by moderate correlations of EC with Na+ and Cl−. Bivariate Gibbs diagrams and ionic ratios indicate silicate weathering and ion exchange as the primary geochemical processes controlling solute concentrations in both aquifers. However, in the Ilhas aquifer, a subordinate contribution from reverse ion exchange is indicated by weak (TDS–Na+, TDS–K+, Na+–Ca2+, K+–Ca2+) and positive TDS–Ca2+ and TDS–Mg2+ correlations. Conversely, negative chloroalkaline indices and the moderate Na+–Cl- correlation indicate that reverse ion exchange processes are mostly absent in the São Sebastião aquifer. Instead, both chloroalkaline imbalance reactions and silicate weathering contribute equally to the observed geochemical patterns. Groundwater geochemical signatures indicate recharge on flexural margins, active water-rock interaction in large depocenters, and mixing of hydrogeochemical facies between aquifer units. These insights contribute to a comprehensive understanding of groundwater evolution, crucial for effective water resource management in the region.