Several studies on geosynthetic clay liners (GCLs) have been conducted on engineering behavior such as hydraulic conductivity and swell index in the presence of alkaline metals (K+ , Mg2+ , Na+ , Ca2+ ) and municipal solid wastes. However, the transport of metals in GCLs holding excavated rocks from mining or construction with the potential of acid and heavy metal generation (acid rock drainage, ARD) has been little studied. This paper aims to explain the impact of ARD on GCLs when applied in rock storage facilities in terms of hydraulic performance and chemical compatibility. The hydraulic conductivity of GCLs may increase from one to three orders of magnitude when permeated with ARD. The metal attenuation or retention in GCLs takes place through four possible mechanisms: cation exchange or unspecific sorption, specific sorption, surface precipitation and co-precipitation. The transport of heavy metals in bentonite consists of three main processes: advection, diffusion and chemical reaction.