Sečovlje Salina is in worldwide unique places. Saline sediment (saline healing mud or “fango”) from the Sečovlje Salina is traditionally used in the coastal health resorts as a virgin material for medical treatment, wellness and relax purposes. Therapeutic qualities of the healing mud depends on its mineralogical composition and physical, mineralogical, geochemical and biological properties. Their microbial and potentially toxic elements contamination are the most important features affecting user safety. However, the degree of metal toxicity (and its regulation) for natural healing mud is still under discussion. Therefore, the influence of the overlying water salinity on the mobility of heavy metals (and some other geochemical characteristics) was studied for saline sediment of the Sečovlje Salina. Experiments takes place in eight tanks under defined conditions i.e. at day (21 °C): night (16 °C) cycle for three months. Sediment, sampled in Sečovlje Salina, was covered with water of different salinities and mixed/stirred every week during the experimental period. Salinity and maturation of sediment does not significantly affect its mineral composition. In the water phase, concentrations of most elements (As, Ba, Cu, Mo, Mn, Ni, Sr, Sb) rise from the beginning to the end of the experiment, whereas the heavy metals (potentially toxic elements) decreasing trend in sediment was observed at that time. Enrichment factor (EF) was under 1 value for Ba, Sr, Mn, which means that the salt mud is not enriched with stated elements. Elements Co, Cr, Cu, Ni, Pb, Zn had EF value under 3, which means that sediments have small enrichment with these elements.