The aim of the research has been to assay the contents of Zn, Cu, Mn, Fe, and Pb in soil and in the organs of wild Thymus serpyllum L. acquired from three natural habitats from the Kuyavia-Pomerania Province (Poland) not exposed to contamination with metals. As compared with the contents of the geochemical background of the soils in the region and the value of enrichment factor (EF), there was noted a considerable content of Pb in the soil from two locations. The Pb content in plant tissues in one of the three locations was higher than the admissible content specified by the World Health Organization WHO (above 10 mg kg−1 d.w.). As for the Zn content, only the plants from the locations with the relatively youngest phytocenosis met the conditions for herbs to be used for phytotherapy. The Zn content in the dry weight of the plants collected from the other two locations exceeded 50 mg kg−1. The risk of an elevated content of Zn and Pb in the plants makes it necessary to monitor the soil environment and to limit the collection of the plants from natural habitats, as well as to encourage the collection from controlled habitats.