Mercury is one of the most toxic and unnecessary elements for human body in a way that only slight amount of it can cause serious hygienic problems and environmental pollution. In the present study, magnetized single walled carbon nanotubes (SWCNTs) functionalized by polydopamine was employed for elimination of mercury heavy metal ions from aqueous media. In order to characterize the physical and chemical properties of the SWCNT and to confirm the functionalization steps, different analyses including TEM, SEM, VSM, EDS, FT-IR were utilized. In the present paper, the effects of experimental parameters such as adsorbent dosage, solution pH, metallic ion initial concentration, process thermodynamics and desorption mechanism on batch system were widely studied. In addition, mercury adsorption trend in continuous system was investigated by a fixed bed reactor. Comparison of adsorption process kinetics were done with models of Freundlich, Langmuir and Dubinin–Radushkevich in batch system and consistency with Yan and Thomas models in continuous system by Sigma plot and MATLAB software packs. Isotherm studies and adsorption kinetics revealed that mercury ions follow Freundlich adsorption isotherm and pseudo-second-order kinetic model. Moreover, thermodynamic studies showed that mercury ion adsorption is an exothermic and spontaneous reaction. Although Thomas model was found to predict more exact results for maximum mercury ion adsorption, both Thomas and Yan models had good fitness with fixed bed reactor data. Finally, adsorption process demonstrated that removal efficiency of the prepared adsorbent was so much higher than raw SWCNTs.