In the present study, a novel and high efficient magnetic alginate beads containing Fe₅C₂@SiO₂ nanoparticles (NPs) were synthesized and applied to remove Cu (II) ions from water. The synthesized Fe₅C₂@SiO₂ NPs were characterized by scanning electron microscopy (SEM) and Transmission electron microscopy (TEM). The elemental content of the magnetic/alginate beads before and after Cu(II) adsorption was analyzed using energy dispersive X-ray spectroscopy (EDS). The influence of important factors such as pH, contact time and initial Cu (II) concentration on the adsorption capacity of magnetic/alginate beads was investigated. The maximum adsorption percent (97.4%) was attained in the pH range of 3–4 and the adsorbent dosage of 0.41 g/L in the Cu (II) concentration of 200 mg/L. Moreover, the maximum capacity of adsorption was compared with silica coated iron carbide alginate and alginate alone. The results showed with adding a 1 mg of silica coated iron carbide NPs to sodium alginate enhanced the adsorption capacity of copper ions to ca. 2 times. The Sips isotherm model was best fitted to the experimental data with the maximum adsorption capacity of 37.73 mg/g for each layer. The adsorption kinetic followed the pseudo-second order kinetic model. These results reveal that the alginate Fe₅C₂@SiO₂ beads could be a candidate for copper ions removal from aqueous solutions.