The toxicity of metal ions on ecosystems has led to increasing amounts of research on their removal from wastewater. This paper presents the efficient application of a carbon magnetic nanocomposite as an adsorbent for the elimination of metal ions (copper, lead and zinc) from aqueous solutions. A Box–Behnken factorial design combined with the response surface methodology was conducted to investigate the effect and interactions of three variables on the pollutant removal process. Highly significant (p < 0.001) polynomial models were developed for each metal ion: the correlation coefficient was 0.99 for Cu(II) and Pb(II), and 0.96 for Zn(II) ion removal. The experimental data were in agreement and close to the theoretical results, which supports the applicability of the method. Working at the natural pH of the solutions, with a quantity of carbon magnetic nanocomposite of 1 g/L and a metal ions’ concentration of 10 mg/L, for 240 min, removal efficiencies greater than 75% were obtained. The kinetic study indicated that a combination of kinetic models pseudo-second order and intraparticle diffusion were applied appropriately for copper, lead and zinc ion adsorption on carbon magnetic nanocomposite. The maximum adsorption capacities determined from the Langmuir isotherm model were 81.36, 83.54 and 57.11 mg/g for copper, lead and zinc ions. The average removal efficiency for five adsorption–desorption cycles was 82.21% for Cu(II), 84.50% for Pb(II) and 72.68% for Zn(II). The high adsorption capacities of metal ions, in a short time, as well as the easy separation of the nanocomposite from the solution, support the applicability of the magnetic carbon nanocomposite for wastewater treatment.