The hydrogeochemical processes and natural background levels (NBLs) of chromium in the ultramafic environment of Vermio Mountain, Western Macedonia, Greece, were studied. Seventy groundwater samples were collected from 15 natural springs between 2014–2020, and an extensive set of physical and chemical parameters were determined. The ultramafic-dominated environment of western Vermio Mt. favors elevated groundwater concentrations of dissolved magnesium (Mg²⁺), silicon (Si), nickel (Ni), and Cr in natural spring waters. Chromium was the principal environmental parameter that exhibited a wide range of concentrations, from 0.5 to 131.5 μg/L, systematically exceeding the permissible limit of 50 μg/L for drinking water. Statistical evaluation of hydrogeological, hydrochemical, and hydrological data highlighted the water-ultramafic rock process as the predominant contributor of Cr in groundwater. The NBL assessment for Cr and Cr(VI) was successfully applied to the typical ultramafic-dominated spring “Potistis” that satisfied all the methodology criteria. The NBLs of Cr and Cr(VI) were defined at 130 μg/L and 100 μg/L, respectively, revealing that a natural ultramafic-dominated environment exhibits the geochemical potential to contribute very high concentrations of geogenic Cr to groundwater. The holistic methodology, proposed herein, could be implemented in any catchment scale to assess geogenic and anthropogenic Cr-sources that degrade groundwater quality.