This investigation was carried out in the Guarani Aquifer System (GAS) following a transect in São Paulo State, Brazil, and involved the analysis of trace elements, REEs and stable isotopes (B, Sr) in both rainwater and groundwater samples (the latter sampled from tube wells drilled in 10 cities). The Brazilian Code for Mineral Waters (BCMW) has been adopted for classifying the groundwaters according to their temperature, and was useful for identifying the major trends of the hydrochemical data. Three water categories are identified: (<25°C), hypothermal (values ranging from 25 to 33°C) and hyperthermal (>38°C). The hyperthermal waters exhibited geostatic pressures >250 bar, whereas the cold/hypothermal waters values <100 bar. REEs concentrations were higher at the monitoring point BCS (Bernardino de Campos). Dissolved strontium in the groundwater behaves like other alkaline earth metals (calcium and barium) in samples collected along the studied transect. The hyperthermal waters tended to exhibit similar 87Sr/86Sr ratios (between 0.7088 and 0.7099), approximately corresponding to the value of ca. 0.709 for seawater Sr isotopic ratio at the end of the Proterozoic. The cold and hypothermal waters exhibited lower B contents than the hyperthermal waters. The δ11B ranged from -8.1 to +12.0‰, where the δ11B-values in cold/hypothermal waters were characteristically positive in clear distinction to the negative δ11B signatures found in hyperthermal waters.