In this study, two natural deep eutectic solvents (NADESs) were prepared from natural hydrogen bond donors (HBDs) based on sugar, namely fructose and sucrose, alongside H2O, and choline chloride as a hydrogen bond acceptor (HBA). The prepared NADESs were used as functionalizing agents with multiwall carbon nanotubes (MWCNTs), and the functionalized MWCNTs were used as adsorbents of Pb(II) lead ions from aqueous solution. The analyses demonstrated that MWCNTs functionalized with sucrose-based NADES to have more sub-stems and functional groups than the MWCNTs functionalized with fructose-based NADES, providing more possible sites for Pb(II) adsorption. The time dependence of Pb(II) adsorption onto these novel adsorbents was found to be better described by a pseudo-second-order kinetic model. Additionally, the Langmuir model better fits the adsorption data due to its higher coefficient of determination. Finally, the operating conditions (pH, adsorbent concentration, and contact time) were optimized using the Box-Behnken model, which demonstrated pH to exert greater influence on the adsorption process than the other studied factors. To the best of our knowledge, this study is the first to apply NADESs as emerging functionalizing agents for carbon nanomaterials in the removal of heavy metals from synthetic wastewater.