Natural clays were used as adsorbent to remove ciprofloxacin from aqueous solutions by adsorption. The textural, structural, and morphological properties were examined, finding low-moderate specific surface area values (9.9–50.1 m2g−1) and a structure coincident with the smectite phase. Adsorption kinetic studies revealed that clay 3 and 4 reached a CIP removal around 70–80 % in 7–8 h. Elovich and pseudo-second-order models were the most suitable to describe the kinetics. The highest equilibrium adsorption capacities (qe = 150.2–193.7 mg g−1) were obtained for clay 1, 3, and 4; the lowest (qe = 30.6 mg g−1) was found for clay 2, which showed the highest-ordered structure. The Freundlich adsorption model led to the best-fitting results. From pH studies, working at solution pH = 4.0 led to the best adsorption results. The estimated thermodynamic parameters suggested that the adsorption process can be considered of physical nature. It was found that the high concentration of CO32– salts in the hospital wastewater effluent enhanced the CIP adsorption capacity, showing a CIP removal of about 95 % for the clay 3. Therefore, the adsorbent with the greatest compromise situation among all the variables was clay 3, presenting the maximum CIP removal after 7 h at pH 4.0, 50 °C and real matrices. The reusability of natural clays can be successfully regenerated by NaOH treatment using the adsorption/desorption process, an indication of its excellent reusability and stability during the regeneration. Finally, DFT molecular studies were performed to clarify the particularities of the adsorption of CIP onto clays.