The aim of this study was to evaluate the mobility of copper (Cu) and zinc (Zn) and their impact on the properties of bentonites and unfrozen water content. Limited research in this area necessitates further analysis to prevent the negative effects of metal interactions on bentonite effectiveness. Tests involved American (SWy-3, Stx-1b) and Slovak (BSvk) bentonite samples with Zn or Cu ion exchange. Sequential extraction was performed using the Community Bureau of Reference (BCR) method. Elemental content was analyzed via inductively coupled plasma optical emission spectrometry (ICP-OES). Unfrozen water content was measured using nuclear magnetic resonance (1H-NMR) and differential scanning calorimetry (DSC). Results showed a significant influence of the main cation (Zn or Cu) on ion mobility, with toxic metal concentrations increasing mobility and decreasing residual fractions. Mobile Zn fractions increased with larger particle diameters, lower clay content, and shorter interplanar spacing, while the opposite was observed for Cu. Zn likely accumulated in larger clay pores, while Cu was immobilized in the bentonite complex. The stability of Zn or Cu ions increased with higher clay content or specific surface area. Residual Zn or Cu fractions were highest in uncontaminated bentonites with higher unfrozen water content, suggesting the potential formation of concentrated solutions in sub-zero temperatures, posing a threat to the clay–water environment, especially in cold regions.