Water pollution has invaded seas, rivers, and tap water worldwide. This work employed commercial Mesquite charcoal as a low-cost precursor for fabricating Mesquite carbon nanoparticles (MUCNPs) using a ball-milling process. The scanning electron energy-dispersive microscopy results for MUCNPs revealed a particle size range of 52.4–75.0 nm. The particles were composed mainly of carbon with trace amounts of aluminum, potassium, calcium, titanium, and zinc. The X-ray diffraction peaks at 26.76 and 43.28 2θ° ascribed to the (002) and (100) planes indicated a crystalized graphite phase. Furthermore, the lack of FT-IR vibrations above 3000 cm−1 showed that the MUCNPs were not functionalized. The MUCNPs’ pore diameter, volume, and surface area were 114.5 Ǻ, 0.363 cm3 g−1, and 113.45 m2 g−1. The batch technique was utilized to investigate MUCNPs’ effectiveness in removing chlorohexidine gluconate (CHDNG) from water, which took 90 min to achieve equilibrium and had an adsorption capacity of 65.8 mg g−1. The adsorption of CHDNG followed pseudo-second-order kinetics, with the rate-limiting step being diffusion in the liquid film. The Langmuir isotherm dominated the CHDNG adsorption on the MUCNPs with a correlation coefficient of 0.99. The thermodynamic studies revealed that CHDNG adsorption onto the MUCNPs was exothermic and favorable, and its spontaneity increased inversely with CHDNG concentration. The ball-milling-made MUCNPs demonstrated consistent efficiency through regeneration–reuse cycles.