This paper investigates the occurrence of internal erosion and the variation of the permeability of geosynthetic clay liner (GCL) with respect to its geotextile component, polymer type and polymer amount added to its bentonite component, hydraulic head, and subgrade material by performing extensive triaxial permeability tests on the GCL specimens. To do this, Na carboxymethyl cellulose (CMC) and polyacrylamide (PAM) were treated with the bentonite component of the GCLs. Then, the GCLs were placed over poorly graded gravel (GP) and poorly graded sand (SP). Consequently, they were tested with two different woven geotextile components under the hydraulics heads of 0.3 m and 10 m. Results showed that only GCLs tested with woven geotextile, having lower tensile strength, lower mass/area and lower thickness over the gravel at a hydraulic head of 10 m, experienced internal erosion. Critically, Na CMC and PAM treatment caused 2–2.5 orders of magnitude decrease in the permeability. Actually, 2% Na CMC and 1% PAM treatment by dry mass were found to be the optimum polymer contents. Both the environmentally friendly biopolymer Na CMC and the synthetic polymer PAM can effectively be treated with Ca bentonite to enhance the hydraulic performance of the GCLs.