The accumulation of heavy metal in soils is a serious environmental problem. The aim of this paper was to compare the adsorption mechanism of ionic polyacrylamides (PAMs)—anionic and cationic with different contents of functional groups, on the surface of clay minerals—montmorillonite (type 2:1) and kaolinite (type 1:1), without and with the presence of heavy metal ions (Cr(VI) or Pb(II)). The dependence of solution pH, structure of mineral, type of PAM, ionic form of heavy metal, as well as order of adsorbates addition on the adsorption efficiency and stability of the clay mineral-polymer-heavy metal system was determined. In addition to adsorption and stability studies, electrokinetic and potentiometric titration measurements were performed. It was shown that the mixed PAM+heavy metal adsorption layers modify the surface properties of clay minerals significantly, which in many cases leads to the effective destabilization of the solid suspension and its separation from the liquid phase. Moreover, the most important factor, which influences the adsorbed amount of ionic polyacrylamide, turned out to be the internal structure of layered aluminosilicates and the presence of inter-package spaces capable of adsorbate molecules accumulating. For this reason the obtained adsorption capacity of montmorillonite is about 100 times higher in comparison to kaolinite.