The simulation-optimisation models of groundwater and contaminant transport can be a powerful tool in the management of groundwater resources and remediation design. In this study, using Multiquadratic Radial Basis Function (MRBF) a coupled groundwater flow and reactive transport of contaminant and oxidant was developed in the framework of the Meshfree method. The parameter analysis has determined the optimum shape parameter (0.97), and the results of the model were compared with a physical sandbox model which were in good agreement. The genetic algorithm approach was used to find the optimum design of the remediation using permanganate as an oxidant. To find the optimum design we considered two objectives and two constraints. The results revealed that the breakthrough of contaminant to the downstream area of interest and the concentration of the contaminant in this area is reduced significantly with optimisation.