The distribution of the high concentrations of arsenic (As) and fluoride (F-) in groundwater on a Pan-European scale could be explained by the geological European context (lithology and structural faults). To test this hypothesis, seventeen countries and eighteen geological survey organizations (GSOs) have participated in the dataset. The methodology has used the HydroGeoToxicity (HGT) and the Baseline Concentration (BLC) index. The results prove that most of the waters considered in this study are in good conditions for drinking water consumption, in terms of As and/or F- content. A low proportion of the analysed samples present HGT≥ 1 levels (4% and 7% for As and F-, respectively). The spatial distribution of the highest As and/or F- concentrations (via BLC values) has been analysed using GIS tools. The highest values are identified associated with fissured hard rock outcrops (crystalline rocks) or Cenozoic sedimentary zones, where basement fractures seems to have an obvious control on the distribution of maximum concentrations of these elements in groundwaters. Display omitted •Geological context is crucial in the spatial analysis of arsenic and fluoride.•HydroGeoToxicity (HGT) assesses quality of groundwater as drinking-water.•BaseLine Concentration (BLC) give the most significant geogenic anomalies.•Structural control is relevant in the distribution of arsenic in porous aquifers.•Lithology is pivotal in fluoride distribution (e.g. fissured hard rocks).