Hydraulic conductivity tests were conducted on six bentonite-polymer (B–P) geosynthetic clay liners (GCLs) to investigate the effect of the slow cation exchange process and polymer elution on the long-term hydraulic conductivity of B–P GCLs. Tests were conducted up to 1458 days and as many as 443 pore volumes of flows (PVFs). Three B–P GCLs consist of linear polymer whereas the other three have crosslinked polymer. One sodium geosynthetic clay liner (Na–B GCL) was used as a control. Hydraulic conductivities (K6766) of B–P GCLs (5.4 × 10−12 m/s to 3.7 × 10−11 m/s) per ASTM D6766 were approximately 2-3 orders of magnitude lower than that of Na–B GCL (2.3 × 10−9 m/s to 3.5 × 10−9 m/s). Tests were continued after hydraulic and chemical equilibrium to investigate the long-term hydraulic conductivity of GCLs. Hydraulic conductivities of GCLs had an increasing trend after hydraulic and chemical equilibrium. The ratio of KL/K6766 for B–P GCLs was 3.5–14.7, whereas ratio of KL/K6766 for Na–B GCLs was 1.0–1.7. Total organic carbon (TOC) tests results confirmed that polymer elution occurred during the entire permeation process. The higher ratio of KL/K6766 for B–P GCLs was attributed to the effect of polymer elution.