Central composite design (CCD) was employed to investigate the adsorption of Pb(II) and Zn(II) metal ions as well as methylene blue (MB) as an aromatic anion by a new EDTA/MnO2/CS/Fe3O4 synthesized nanocomposite. The effect of possible affective factors including contaminant concentration (20-200 mg/L), pH (2-8), adsorbent content (0.1-0.9 g/L), and contact time (10-110 min) were studied on the adsorption of the metal ions using response surface methodology (RSM). The highest removal percentages predicted by the model were 100.776% and 87.069%, respectively, for the removal of Pb(II) and Zn(II), that the value of more than 100% in the case of Pb(II) was due to the model error. The effect of the simultaneous presence of methyl blue (MB) and the metal ions in the aqueous solution on the adsorption rate of each metal ion was investigated. The study of adsorption isotherms in the single-component adsorption showed the dominance of Langmuir isotherm over the adsorption process of each pollutants (R2>0.99). The maximum adsorption capacities according to the Langmuir model were 310.4 and 136 mg/g for lead and zinc ions, respectively, and 421.1 mg/g for methyl blue. The results showed that the studied nanocomposite still has high efficiency after five consecutive adsorption-desorption cycles.