Since organic dyes are the main component of many industrial wastes, it is necessary to be removed efficiently and instantaneously. The aim of this research focuses on the synthesizing of organoclay by modifying kaolinite with cetyl trimethyl ammonium bromide and applying it for the removal of (methyl-orange) dye from water by the mechanisms of adsorption. The effects of several parameters, mainly agitation time, water pH, adsorbent doses, and dye concentrations, on the adsorption process were optimised using the central composite design (CCD) method, which was performed using MINITAB package (version 17). Results showed that the dye was completely (100%) removed at pH of 4.0, adsorbent dose of 0.4 g, dye concentration of 50 mg/L, and agitation speed of 160 rpm. In addition, it was found that Freundlich and Sips isotherms were the best models to track lab data. Moreover, the Pseudo second order method was found to be more convenient compared to other models for studying kinetics of the sorption mechanism. For column testing, an appropriate hydraulic conductivity and reactivity were obtained by combining modificatory kaolinite and glass waste with weight proportions of 50:50. Thus, empirical simulations such as those in the kinetic model of Clark have provided satisfactory consent for using the simulated methyl orange.