Gold mining activities are undertaken both at large and artisanal scale, often resulting in serious ‘collateral’ environmental issues, including environmental pollution and hazard to human and ecosystem health. Furthermore, some of these activities are poorly regulated, which can produce long-lasting damage to the environment and local livelihoods. The aim of this study was to identify a new workflow model to discriminate anthropogenic versus geogenic enrichment in soils of gold mining regions. The Kedougou region (Senegal, West Africa) was used as a case study. Ninety-four soil samples (76 topsoils and 18 bottom soils) were collected over an area of 6,742 km2 and analysed for 53 chemical elements. Robust spatial mapping, compositional and geostatistical models were employed to evaluate sources and elemental footprint associated with geology and mining activities. Multivariate approaches highlighted anomalies in arsenic (As) and mercury (Hg) distribution in several areas. However, further interpretation with enrichment factor (EFs) and index of geoaccumulation (IGeo) emphasised high contamination levels in areas approximately coinciding with the ones where artisanal and small scale mining (ASGM) activities occur, and robust compositional contamination index (RCCI) isolated potentially harmful elements (PHE) contamination levels in very specific areas of the Kedougou mining region. The study underlined the importance of complementary approaches to identify anomalies and, more significantly, contamination by hazardous material. In particular, the analyses helped to identify discrete areas that would require to be surveyed in more detail to allow a comprehensive and thorough risk assessment, to investigate potential impacts to both human and ecosystem health.