Functionalization of multi-walled carbon nanotubes can be carried out by introducing amino and thiol functional groups onto the nanotube sidewalls. This functionalized multi-walled carbon nanotubes can be used as a new type of efficient metal ions adsorbent from aqueous solutions. In this study, batch and column adsorption experiments were carried to evaluate the adsorption capacities of single and binary system mercury and cadmium. In the single system, the maximum adsorption capacity of 204.64 and 61.10 mg/g were obtained for mercury and cadmium, respectively, while for binary systems, the values of 35.89 and 14.09 mg/g were achieved for mercury and cadmium, respectively. Column breakthrough curves were obtained and described by Yan and Thomas models. The bigger Thomas rate constant (kTh) (120.77 ml/min/mg for Cd(II) and 9.44 ml/min/mg for Hg(II)) indicated that the intensity of adsorption of Cd(II) onto thiolated MWCNTs was higher compared to Hg(II). However, the value of maximum adsorption capacity (qe) for Hg(II) (39.75 mg/g) was bigger than that of Cd(II) (9.72 mg/g) in continuous system.