A novel polyaniline-modified CNT and graphene-based nanocomposite (2.32–7.34 nm) was prepared and characterized by spectroscopic methods. The specific surface area was 176 m2/g with 0.232 cm3/g as the specific pore volume. The nanocomposite was used to remove zinc and lead metal ions from water; showing a high removal capacity of 346 and 581 mg/g at pH 6.5. The data followed pseudo-second-order, intraparticle diffusion and Elovich models. Besides this, the experimental values obeyed Langmuir and Temkin isotherms. The results confirmed that the removal of lead and zinc ions occurred in a mixed mode, that is, diffusion absorption and ion exchange between the heterogeneous surface of the sorbent containing active adsorption centers and the solution containing metal ions. The enthalpy values were 149.9 and 158.6 J.mol−1K−1 for zinc and lead metal ions. The negative values of free energies were in the range of −4.97 to −26.3 kJ/mol. These values indicated an endothermic spontaneous removal of metal ions from water. The reported method is useful to remove the zinc and lead metal ions in any water body due to the high removal capacity of nanocomposite at natural pH of 6.5. Moreover, a low dose of 0.005 g per 30 mL made this method economical. Furthermore, a low contact time of 15 min made this method applicable to the removal of the reported metal ions from water in a short time. Briefly, the reported method is highly economical, nature-friendly and fast and can be used to remove the reported metal ions from any water resource.