Abstract: A composite liner consisting of a geomembrane (GMB) and a geosynthetic clay liner (GCL) can be compromised by inorganic contaminants because of a defective GMB. When the composite liner with defective GMB is exposed to aggressive leachate conditions, the neglect of the chemical incompatibility of the GCL can potentially result in an underestimation of the leakage rate and flux through the composite liner. In this paper, a numerical investigation of the effect of chemical incompatibility of GCL on the barrier performance of the composite liner with hole-defective GMB was conducted via four cases with leachate solutions having varied cation valencies and ionic strengths, in which the hydraulic conductivity of GCL was concentration-dependent. Both the effect of the chemical incompatibility of GCL and the mechanisms causing the effect were analyzed. The incompatibility of GCL resulted in significant increases in leakage rate and flux through the composite liner by factors of up to 4.9 and 5.0, respectively. The incompatibility-affected area in GCL is located within 0.1 m from the center of the hole in the GMB. The coupled increase in the hydraulic conductivity of GCL and pore water concentration impacts the flux and leakage in a short period of time. With GCL chemical incompatibility considered, advection may dominate the contaminant transport through GCL.