Clinoptilolite, a naturally occurring zeolite with unique adsorption properties, is investigated in its nanoscale form as a sustainable adsorbent for effectively removing contaminant dyes, rhodamine B (RhB), malachite green (MG), and methyl green (MeG), from aqueous solutions. The nano clinoptilolite was prepared by ball milling and characterized using various techniques including XRD, FTIR, SEM, TGA, BET, and zeta potential to confirm its structure, functional groups, porous morphology, thermal stability, surface area and pore size distribution, and surface charge, respectively. The nano clinoptilolite has a crystalline size of 19.5 nm, determined by XRD. Its average hydrodynamic size in water is 285 nm, measured by dynamic light scattering. Adsorption experiments were carried out to evaluate the dye removal efficiency under various conditions such as pH, zeolite dose, dye concentrations, and contact time. The equilibrium adsorption data were fitted with different isotherm models such as Freundlich, Langmuir, Langmuir-Freundlich, and Sips; and the kinetics adsorption data were fitted with pseudo-first-order, pseudo-second-order, mixed-order, and Avrami models. Nanosized clinoptilolite exhibited a high maximum adsorption capacity for MG (191.36 mg MG/g at pH 5.0), exceeding a previous report by 336 % (43.86 mg MG/g). RhB adsorption capacity on zeolite was 58.02, 24.28 mg/g at pH 3.0, 7.0, and MeG was 162.94 mg/g at pH 7.0. Finally, Monte Carlo and molecular dynamics simulations were used to elucidate the specific binding sites, adsorption energies, and mechanisms involved in the removal process.