The present study evaluated the spatiotemporal variation in concentration of cadmium, lead and copper ions in groundwater wells in the stratigraphic subdivision “Santo Anastácio” that belongs to the Bauru aquifer system in the western region of São Paulo State. Exploratory statistics methods were employed to investigate the response of the concentration of these metals in the aquifer through the pluviometric index of the region. The results show a direct dependence of the mean monthly flow of the metals in the groundwaters to the monthly rainfall flow. The observed behavior was cyclic with a gradual increase and decrease in the flow throughout time. Two groups of cyclic variation were identified. The seasonality of the mean monthly flow of Cd2+ and Pb2+ was inversely proportional to the magnitude of the pluviometric index of the region studied. Meanwhile, the seasonality of Cu2+ was directly correlated to the seasonable rainfall variability. These behaviors lead us to point out that cadmium and lead come from minerals present in the aquifer itself and the presence of copper in groundwater is associated with an anthropogenic action due to the region’s agricultural activity. The study helps us better comprehend the behavior of the whole groundwater system through a comparison with temporal hydrogeochemistry.