Establishing the contribution of natural enrichment of a substance and anthropogenic inputs has become a major issue for the management of groundwater systems. The issue is made more complex when the geology of the concerned territories is heterogeneous, at variable geographical scales, at a site that has experienced mining activity that has left behind mining remains. Several studies have tried to answer this problem using different approaches: statistical, geostatistical, geological, and geochemical. The limits of these studies are seen through the incomplete integration of geological and geomorphological parameters in the results. The aim of the present research is, therefore, to look deeper into an approach to estimate the respective contributions of the natural geochemical background and anthropogenic inputs, by simultaneously considering the heterogeneity of the geology, the variability of the spatial scale, and the combination of geological, geomorphological and statistical factors. A multi-criteria aggregation operator was thus developed and implemented on underground water bodies delimited by the Gardon watershed in the Cevennes (a region with former mining activities — France), in order to produce quantitative and qualitative maps for discriminating between the natural geochemical background and anthropogenic inputs. 176 geochemical observation points on groundwater quality were collected by sampling and through the acquisition of public data on water sources (ADES database), wells and boreholes, to reconstruct the spatial distribution of arsenic and antimony in the study site. An aggregation operator was developed, which enabled the determination of the formulae to calculate the natural geochemical background and hence deduce the anthropogenic contributions. Cartography of the quantitative and qualitative aspects of the geochemical concentrations that have been impacted by anthropogenic activity made it possible to determine remarkable focal points located on the Cevennes fault and other specific points of geochemical interest.