Migration of chloride inorganic contaminants through a single hole in a geomembrane (GMB) in direct contact with a geosynthetic clay liner (GCL) and an adjacent silty sand is simulated using the 3D HydroGeosphere code. The hole in the GMB is 10 mm in diameter and the applied hydraulic heads are 0.3 and 1 m. Numerical Simulations were performed in order to predict contaminants behaviour to reach complete diffusion of a specific concentration of sodium chloride (NaCl) into the GCL and the soil liner and to compare numerical concentrations with experimental values. Obtained results of NaCl concentrations through the GCL and the subsoil were compared to existing results in order to validate the ability of the used code to predict contaminant transfers through a single hole in the GMB by the coupled phenomena of diffusion and advection. Results of numerical simulations of relative concentrations with time are in good agreement with the theoretical curve for advection-diffusion transport. Furthermore, results of simulated contaminant concentrations agree with observed values for diffusion coefficient of 6×10-10 m2/s for the soil and 1×10-10 m2/s for the GCL when the hydraulic head is 0.3m and 8×10-10 and 4×10-10 m2/s respectively for the soil and GCL for a 1m applied hydraulic head at the hole. The use of the HydroGeosphere code thus seems on the basis of this study to constitute a new potential tool for giving predictions of effluent concentration with time and chloride distribution in the silty sand in contact with the composite liners that prove to be in good agreement with experimental results from previous studies.