Water purification techniques, including membrane technologies, ion exchange and adsorption, chemical/biochemical reduction, and electrochemical processes, have been developed to remove/recover metal ions species from polluted wastewater. This work assessed the efficiency of polymeric, biodegradable, ultra‐permeable and magnetic nanocomposite membrane (CNCs/N6@Fe3O4‐CT) in a continuous packed bed column for the removal of Cd(II), Cr(VI), and Pb(II) metal ions from synthetic wastewaters. The eco‐compatibility of CNCs/N6@Fe3O4‐CT was increased using chitosan biopolymer. Fe3O4 nanoparticles increased the surface area and improved the separation process. CNCs and N6 polymeric materials enhanced their strength, porosity, and additional binding sites. The CNCs/N6@Fe3O4‐CT nanocomposite membrane was employed as packing material in a fixed‐bed lab‐scale column (height 30 cm, diameter 1.5 cm) to constantly remove Cd(II), Cr(VI), and Pb(II) metal ions from synthetic wastewaters and actual hexavalent chromium tannery effluent. The studies were carried out with different initial metal ion concentrations (10, 20, and 30 mg/L), input flow rates (2, 4, and 6 mL/min), and solution pH values (2.0, 5.0, and 8.0). The obtained experimental data from the breakthrough curves was fitted to the traditional dynamic Thomas model, Yoon‐Nelson, and Bed Depth Service Time (BDST) model.