Calcareous and smectitic clay samples from the Coniacian–Lower Campanian system, Tunisia, were used as adsorbents for the removal of copper and zinc from aqueous solutions in single and binary systems. Calcareous clay sample was treated with acetic acid to obtain carbonate-free sample that was also used for metals removal. The adsorption of metal ions onto natural clay was tested in a batch method by mixing 1 g/L of each sample with a metal ion solution of zinc (300 μmol/L) and/or copper 600 μmol/L under the operating pH of 6, and agitation speed of 200 rpm within the equilibrium time of 60 min at 25 °C for single and binary systems. Our results showed that natural clay samples were mainly composed of silica, alumina, iron, and magnesium oxides. Adsorption data showed that the studied clay samples removed substantial amounts of heavy metals in single and mixed systems. Initial solution pH and carbonates contents enhanced the removal capacities of the studied clay samples, confirming their strong influencing effects. Thermodynamic parameters indicated an endothermic adsorption for metals removal by calcareous clay, but exothermic process for the smectitic sample. These results suggest that the Late Cretaceous clays, Tunisia, can be effectively used as natural adsorbents for the removal of toxic heavy metals in aqueous systems.