The hydraulic conductivity of geosynthetic clay liners (GCLs) is not fully understood and certain gaps in knowledge are still present, such as the effect of coupled mechanical and chemical processes. The current study aimed to develop a simplified mathematical model to predict the hydraulic conductivity of GCLs, particularly regarding the coupled effects of mechanical and chemical processes. Based on Darcy's Law and Poiseuille’s Law, the method combines diffuse double layer (DDL) theory and fractal theory. External factors such as confining pressure and the concentration of the permeating solution, and inherent properties such as exchangeable cations, ionic radius, montmorillonite surface fractal dimension, the distance between two montmorillonite layers (m) after swelling at the exchangeable cation i (i denotes the primary exchangeable cations, such as Na+, Ca2+, K+, and Mg2+ in bentonite), density, and coefficient of viscosity of interlayer water between two montmorillonite layers, were considered. The proposed theoretical model gave relatively accurate predictions. A practical estimate of GCL hydraulic conductivity was also derived. The predictions were compared with experimental results and good qualitative agreement was found. From the experimental results, the proposed prediction model has a maximum deviation of ~1:10–10:1, and the empirical model has a mean deviation of ~1:15–15:1.