In this study, kaolinite-based clay (Ka-Clay) was used as an adsorbent for the efficient removal of Pb(II), Cd(II) and Hg(II) ions from aqueous media. The selection of Pb(II), Cd(II) and Hg(II) ions for experimental studies took into account their high toxicity, while the choice of Ka-Clay, the ease of preparation and high availability of this material were the most important arguments. Ka-Clay exhibits high adsorption performance, with removal percents over 98% for Pb(II) and 93% for Cd(II), even at high concentrations of metal ions (over 150 mg/L, pH = 6.5, 4 g adsorbent/L, 21 ± 1 °C). For Hg(II) ions, the adsorption percent does not exceed 55%, and this moderate value is mainly due to the significant change in pH. The adsorption behavior was in accordance with the Langmuir model (R² > 0.95) and the pseudo-second order kinetic model (R² > 0.99), indicating an adsorption process that occurs mainly through chemical interactions at the adsorbent surface between the metal ions and the functional groups. Adsorption processes are spontaneous (ΔG = −8.66 ÷ −15.76 kJ/mol) and endothermic (ΔH = 7.09 ÷ 21.81 kJ/mol), and the adsorption mechanism is the results of elementary processes of electrostatic attraction, ion exchange and superficial complexation. The insignificant effect of other ions (Ca(II), Mg(II), Na(I), K(I)) present in real wastewater samples as well as the desorption behavior of exhausted adsorbent highlight the practical utility of this adsorbent on a large scale. The experimental results included in this study suggest that Ka-Clay can be used as a promising adsorbent for the removal of high concentrations of toxic heavy metals with low cost and high efficiency, and this can contribute to the design of a sustainable wastewater treatment method.