The purpose of this study was to determine the effect of copper or zinc ions, absorbed by soil on its physical and physicochemical properties. The change in these properties may reduce the soil usefulness as a mineral protective barrier, for example, on hazardous waste landfills. Parameters such as granulometric composition, effective particle size d, empirical hydraulic conductivity, Atterberg limits, colloidal activity, specific surface area, sorption moisture content, and montmorillonite content were determined. The tests were carried out on model Na or Ca samples of American bentonites (SWy-3, Stx-1b) and Slovak bentonite from Jelšový potok (BSvk), subjected to ion exchange for Cu or Zn ion. The content of elements was determined using inductively coupled plasma optical emission spectrometry (ICP-OES). Regression analysis showed a significant effect of Zn ions on the reduction of sorption moisture content w and the increase in the hydraulic conductivity. Nearly complete negative correlation was obtained between the Cu ion content and the specific surface area, sorption moisture content w, and montmorillonite content (R = -0.99). It was observed that the significance of the influence of Cu and Zn ions on specific clay properties differed, which indicates different behavior of these metals in the clay-water system. The different nature of clays contaminated with Cu and Zn ions justifies the need to continue research on other potentially toxic metals and to further search for prediction equations of the cohesive soil hydraulic conductivity based on soil parameters that are most frequently modified as a result of their impact.