This study aims to specify the source minerals of geogenic chromium in soils and sediments and groundwater and to determine the favorable hydrogeological environment for high concentrations of Cr(VI) in groundwaters. For this reason, chromium origin and the relevant minerals were identified, the groundwater velocity was calculated and the concentrations of Cr(VI) in different aquifer types were determined. Geochemical and mineralogical analyses showed that chromium concentrations in soils and sediments range from 115 to 959mg/kg and that serpentine prevails among the phyllosilicates. The high correlation between chromium and serpentine, amphibole and pyroxene minerals verifies the geogenic origin of chromium in soils and sediments and, therefore, in groundwater. Manganese also originates from serpentine, amphibole and pyroxene, and is strongly correlated with chromium, indicating that the oxidation of Cr(III) to Cr(VI) is performed by manganese–iron oxides located on the surface of Cr–Mn-rich minerals. Backscattered SEM images of the soils revealed the unweathered form of chromite grains and the presence of Fe–Mn-rich oxide on the outer surface of serpentine grains. Chemical analyses revealed that the highest Cr(VI) concentrations were found in shallow porous aquifers with low water velocities and their values vary from 5 to 70μg/L. Cr(VI) concentrations in ophiolitic complex aquifers ranged between 3 and 17μg/L, while in surface water, karst and deeper porous aquifers, Cr(VI) concentrations were lower than the detection limit of 1.4μg/L. Display omitted •Fe–Mn oxides are located on the surface of mafic minerals and coexist with Cr.•Cr(VI) is released directly from serpentine, chlorite, amphibole and pyroxene.•Higher Cr(VI) concentrations are detected in shallow porous aquifer (<150m).•Low groundwater velocity favors Cr(VI) generation in sedimentary aquifer.