The legal regulatory/action levels of trace elements in soils are established at high concentrations, at which the crucial functions of soil are at risk or are eliminated. However, concentrations below these action levels, but above presumed natural levels, may also limit particular ecosystem services, including organic food production. Thus, defining the (ambient) background concentrations is an essential part of environmental or health risk assessment, e.g., on Chernozems, which are considered to be the most productive soils and ones that should be protected against all forms of contamination. Based on 28 profiles of chernozemic soils developed from loess in an agricultural region of SW Poland presumed to be free of industrial contamination, ambient geochemical baselines have been derived for Fe and six trace metals for four standardized soil layers, including the topsoil (plow layer) and parent material layers. The median values for the plow layer (1.89% for Fe, and 537, 49, 17, 14, and 26 mg kg−1 for Mn, Zn, Pb, Cu, and Ni, respectively) are lower than the values reported for other Chernozems in SE Poland/Europe/the world, and thus may serve as a general geochemical baseline for chernozemic soils developed from loess. The concentration of Cd, although lower than in other Chernozems around the world, is higher than in Ukrainian Chernozems and thus may serve as a local (or Central European) baseline only. The median concentrations of Fe, Cu, Mn, and Zn are very close to their concentrations in the Chernozem buried under the Neolithic kurgan. However, Pb and Cd concentrations are two times higher than in the buried soil, indicating the scale of general contamination of the topsoil horizons of arable soils. Concentrations of the elements under study, excluding Fe, in both the buried and surface soils are significantly higher in the topsoil layer compared to parent material (loess), and this justifies the separate baseline values for topsoil horizons, instead of background values derived universally for parent rock types. This is essential, in particular in soils texturally differentiated within profiles, where the subsoil material has a different origin and cannot be considered the parent material for topsoil horizons. Underlying or locally outcropped bedrock (e.g., serpentinite rocks) may naturally enhance the total concentration of trace elements in the entire soil profile by the addition of metal-rich regolith particles during the formation of surface covers, e.g., by eolian processes under periglacial conditions (Late Pleistocene). Such soils are naturally enriched with metals (with nickel in the case of serpentinite bedrock), cannot be considered contaminated, and thus require a separate legal treatment, including separate (or individually suited) background baselines for health risk assessments.