In this study, a facile hydrothermal method was used for the synthesis of Fe3O4@MoS2 magnetic nanoparticles. Then, this compound was used as an efficient adsorbent for the simultaneous removal of Cu(II) and Pb(II) ions from water. The prepared nanoparticles were characterized by scanning electron microscopy, X‐ray diffraction, vibrating sample magnetometer, and Fourier transform infrared spectroscopy. In addition, the effect of operational parameters on the adsorption process, such as initial pH, the concentration of metal ions, and sorbent mass, was investigated. The results of response surface methodology, obtained from Box‐Behnken design, was used to optimize the removal percent (%R) of Cu(II) and Pb(II). The effect of the different variables and their interactions was displayed by a regression model. A good agreement was seen between the proposed quadratic model resulting from Box‐Behnken design approach and the experimental data. According to the obtained results, the optimized conditions for the removal of metal ions were as follows: pH = 3, sorbent dose = 0.05 g, CPb (initial Pb(II) concentration) = 240.70 mg/L, and CCu (initial Cu(II) concentration) = 198 mg/L. The adsorption of both Freundlich and Langmuir isotherm models and pseudo‐second‐order kinetic model described the adsorption process well (R2 > 0.99). The obtained amounts of the thermodynamic parameters, such as ∆G°, ∆S°, and ∆H°, have proved that the adsorption of Pb(II) and Cu(II) ions on the surface of Fe3O4@MoS2 nanoparticles is spontaneous, feasible, and endothermic in nature.