Abstract: A series of flexible-wall permeameter tests is conducted to investigate the effects of confining pressure and chemical solutions on the hydraulic performance of sodium bentonite-based geosynthetic clay liners (GCLs). The results show that under deionized water permeation, the hydraulic conductivity of GCLs decreases logarithmically with increasing confining pressure, indicating strong stress sensitivity. At low to moderate concentrations, divalent cations have a significantly greater detrimental effect on GCL performance than monovalent cations. While NaCl solutions cause less than an order-of-magnitude increase in hydraulic conductivity, CaCl₂ solutions severely suppress the swelling capacity of bentonite, enlarge inter-granular voids, and result in up to five orders of magnitude increase in permeability with rising concentration. Additionally, physical disturbances such as wrinkling lead to non-uniform granular distribution and preferential flow paths, resulting in an approximately one-order-of-magnitude increase in hydraulic conductivity. Under coupled stress–chemical conditions, GCLs exhibit minimal sensitivity to confining pressure in low-concentration or monovalent cation solutions. However, in high-concentration divalent cation environments, increasing the confining pressure can reduce hydraulic conductivity by about three orders of magnitude; yet, the values still fail to meet the Chinese national standard of 10^-11 m/s. At the mesoscale, granular size, spatial distribution, porosity, and the formation of continuous flow channels in bentonite are identified as key factors that governing the structural evolution and eventual hydraulic failure of GCLs.