In this work, acid-functionalized multiwalled carbon (MWCNTs–CO2H) nanotube was successfully functionalized with a heterocyclic scaffold, namely benzimidazole, to give novel functionalized multiwalled carbon nanotubes (BI@MWCNTs). Then, FTIR, XRD, TEM, EDX, Raman spectroscopy, DLS, and BET analyses were used to characterize the synthesized BI@MWCNTs. The effectiveness of the adsorption of two heavy metal ions, Cd2+ and Pb2+, in single metal and mixed metal solutions on the prepared material was investigated. Influencing parameters for the adsorption method, for example duration, pH, starting metal concentration, and BI@MWCNT dosage, were examined for both metal ions. Moreover, adsorption equilibrium isotherms fit with the Langmuir and Freundlich models perfectly, while the intra-particle diffusion models provide pseudo-second order adsorption kinetics. The adsorption of Cd2+ and Pb2+ ions onto BI@MWCNTs revealed an endothermic and a spontaneous method with great affinity as a result of the negative values of Gibbs free energy (ΔG) and the positive values of enthalpy (ΔH) and entropy (ΔS). Both Pb2+ and Cd2+ ions were completely eliminated from aqueous solution (100 and 98%, respectively) using the prepared material. Additionally, BI@MWCNTs have a high adsorption capacity and were regenerated in a simple way and reused for six cycles, which make them a cost-effective and efficient absorbent for the removal of such heavy metal ions from wastewater.