High ammonium (NH4), arsenic (As) and boron (B) concentrations are found in aquifers worldwide and are often related to human activities. However, natural processes can also lead to groundwater quality problems. High NH4, As and B concentrations have been identified in the confined, deep portion of the Niebla-Posadas aquifer, which is near the Cobre Las Cruces (CLC) mining complex. The mine has implemented a Drainage and Reinjection System comprising two rings of wells around the open pit mine, were the internal ring drains and the external ring is used for water reinjection into the aquifer. Differentiating geogenic and anthropogenic sources and processes is therefore crucial to ensuring good management of groundwater in this sensitive area where groundwater is extensively used for agriculture, industry, mining and human supply. No NH4, As and B are found in the recharge area, but their concentrations increase with depth, salinity and residence time of water in the aquifer. The increased salinity down-flow is interpreted as the result of natural mixing between infiltrated meteoric water and the remains of connate waters (up to 8%) trapped within the pores. Ammonium and boron are interpreted as the result of marine solid organic matter degradation by the sulfate dissolved in the recharge water. The light δ15NNH4 values confirm that its origin is linked to marine organic matter. High arsenic concentrations in groundwater are interpreted as being derived from reductive dissolution of As-bearing goethite by dissolved organic matter. The lack of correlation between dissolved Fe and As is explained by the massive precipitation of siderite, which is abundantly found in the mineralization. Therefore, the presence of high arsenic, ammonium and boron concentrations is attributed to natural processes. Ammonium, arsenic, boron and salinity define three zones of groundwater quality: the first zone is close to the recharge area and contains water of sufficient quality for human drinking; the second zone is downflow and contains groundwater suitable for continuous irrigation but not drinkable due to high ammonium concentrations; and the third zone contains groundwater of elevated salinity (up to 5940 μS cm− 1) and is not useable due to high ammonium, arsenic and boron concentrations. © 2015, Elsevier B.V.