The efficiency of two low-cost, abundant and natural clay minerals, palygorskite and vermiculite, in terms of reducing the concentation of Cu2+ and Ni2+ ions was evaluated here. Natural clay minerals were characterized by X-ray powder diffraction (XRD), scanning electron microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), BET specific surface area and pore-diameter analysis. Batch-type experiments were performed and various parameters, i.e. pH, clay amount, contact time and initial metal concentration, that affect adsorption processes were investigated. The adsorption of Cu2+ and Ni2+ ions is pH-dependent, while minor clay quantities were sufficient to achieve high removal efficiencies. Adsorption equilibrium occurred in 60 min and the adsorption kinetics were better described by pseudo-second-order kinetics. Experimental results were analysed by the Langmuir, Freundlich, Dubinin–Radushkevich (D–R), Temkin and Halsey isotherm equations. The release of exchangeable cations (i.e. Ca2+, Mg2+, Na+ and K+) was examined to verify an ion-exchange mechanism.