Groundwater interacts with mineral deposits, making this secondary environment a medium of choice for geochemical exploration. With increasing depth, groundwater in Precambrian shields typically matures and increases in salinity through prolonged water–rock interactions and mixing with geologically old saline fluids. As the focus of mineral exploration is gradually shifting toward deeper targets, the influence of salinity on pathfinder background levels and anomalous thresholds must be considered. We compiled a deep background database (Deep Abitibi Groundwater database; DAGW) containing groundwater samples between depths of 0 m and 690 m from barren exploration boreholes in the Abitibi subprovince, Quebec, to evaluate the natural elemental levels at depth. The DAGW provides valuable knowledge of the base levels of a wide spectrum of elements and of the changes in these base levels along with the increasing salinity in bedrock aquifers of the deep Canadian Shield. This can serve to estimate background values during hydrogeochemical exploration campaigns. The regional Abitibi base level for Zn (median of 7.5 μg/L), a key pathfinder for VMS mineralization, is unaffected by the increasing salinity levels down to depths of 690 m. Hence, down to this depth, the Zn concentrations measured may be used directly for mineral exploration, and no further correction for the effects of salinization is necessary. We conducted a case study near an undisturbed VMS-type deposit (Daniel 25) and a Zn enrichment halo was observed. Within the halo, Zn concentrations increased with depth, indicating that Zn mobility was positively affected by the geochemical conditions of the deeper aquifer. Anomalous Zn thresholds representing the proximal (50–600 m from the mineralization) and direct contact (within 50 m of the mineralization) footprints of the Daniel 25 deposit were estimated at 50 μg/L and 380 μg/L, respectively. An anomalous threshold was also estimated for Co, a secondary pathfinder, at 0.5 μg/L. Unlike Zn, several other elements, which could be used to trace mineral deposits, are affected by salinization. As a final step, we applied a correction to the Daniel 25 data, based on elemental baseline trends observed in the DAGW. The aim was to remove the effects of salinity and enhance the statistical correlations caused by the presence of the mineralized body. This correction led to the emergence of new spatial correlations, notably with Na and Sr, that are coherent with the increasing hydrothermal alteration in proximity to the ore.