The Idrija mine in Slovenia was a significant anthropogenic source of mercury. Although the production in the mine stopped in 1995, the soil in surrounding of Idrija is highly polluted with mercury due to the inefficient ore roasting, so the concentration reaches even up to 10 000 mg Hg/kg. In such karst area, surface and rain waters can leach mercury from contaminated soil to deeper soil layers and then into groundwater. Since mercury is one of the most toxic metals, it is necessary to find an efficient, cost- effective method for its removal from contaminated waters. This paper investigated the efficiency of the natural zeolite clinoptilolite of particle size 0.6 - 0.8 mm in the treatment of the leachate obtained by leaching the mercury contaminated soil of Idrija district. The highest removal efficiency has been obtained in leachates with the lowest concentration of total mercury, which has been decreased to below the maximum permissible concentration. The highest equilibrium quantity of removed total mercury per unit of the zeolite mass has been achieved in the leachates with the highest concentration of total mercury, and decreased by decreasing in initial concentration. The natural zeolite clinoptilolite can be successfully applied for the treatment of mercury contaminated waters, especially in the case of low initial total mercury concentrations. However, in order to increase the efficiency of natural zeolite for total mercury removal, it is necessary to improve the surface properties of zeolite for adsorption of various ionic and organic species, which is most commonly achieved by modification with organic surfactants.