The engineering properties of geosynthetic clay liners (GCLs) are closely related to the chemistry of pore liquid. For applications in lining systems or cover systems of landfills, covers for remediation sites, and secondary containment systems, GCLs are likely to be permeated by more than one type of liquid. In this study, GCL specimens were hydrated and permeated with different liquids. The hydraulic conductivity of these GCL specimens was determined. The results showed that the hydraulic conductivity of GCLs was controlled by both hydrating and permeating liquid. In addition, even if GCLs were hydrated with aqueous phase liquids other than fresh water, they still have the ability to retard infiltration effectively.