Geosynthetic clay liners (GCLs) are used in landfill applications because of their high deformation resistance and excellent self-healing ability. In the present study, air and hydraulic flow characteristics of natural bentonite based GCL (GCL-N) and polymer amended bentonite based GCL (GCL-A) were assessed using air permeability and hydraulic conductivity measurements. The airflow characteristics of GCLs were studied at various apparent degrees of saturation (Sa) and corresponding suction using a custom-designed air permeability test setup. The effect of desiccation on the airflow characteristics of GCL-A was also examined. Further, hydraulic flow characteristics of virgin and desiccated-rehydrated GCLs were assessed using a flexible wall permeameter. The water absorption capacity of GCL-A is relatively higher than GCL-N, irrespective of the stress state. For any chosen Sa, air permeability of GCL-A is lower than GCL-N. Moreover, with the decrease in the suction from 2500 kPa to 1000 kPa, the air permeability of virgin GCL-A has reduced from 9 × 10−12 m2 to 3.57 × 10−16 m2 while the desiccated-rehydrated GCL-A has reduced from 8.86 × 10−11 m2 to 1.9 × 10−13 m2. The hydraulic conductivity of GCL-A is two orders of magnitude less than GCL-N, which shows the better performance of GCL made with amended bentonite.