Geosynthetic clay liners (GCLs) are often used as lining materials for freshwater reservoirs. To irrigate agricultural land without depleting groundwater, surface water is stored in these artificial ponds. In this study, hydraulic conductivity tests were performed on GCLs placed in flexible-wall permeameters under hydraulic heads of up to 50 m in order to investigate the risk of internal erosion. In these tests, base pedestals made of Plexiglas with uniform circular voids were placed beneath the GCLs instead of a typical gravel subgrade. The voids in the base pedestal represented the voids between uniform rounded gravel particles. Different types of GCLs were tested. GCL-1 was reinforced using needle-punching technology, whereas GCL-2, GCL-3, and GCL-4 were un-reinforced GCLs that were assembled in the laboratory. We investigated the effects on internal erosion of the void size in the subbase; the geotextile component that was in contact with the subbase; the bentonite component; and the manufacturing process of the GCLs. Test results indicated that internal erosion was directly related to the void diameter of the base pedestal. The resistance of the needle-punched GCL to internal erosion was better than that of the un-reinforced GCLs. The degree of internal erosion was also related to the engineering properties of the geotextile in contact with the base pedestal. Higher tensile strength of the GCL reduced the possible potential for internal erosion within it. The type of bentonite did not have a significant effect on internal erosion.