This paper provides information on placing geosynthetic clay liner (GCL) as a lining material over coarse-grained soils in cover systems or irrigation ponds. The effects of the hydraulic head acting over the GCL and the void size of the subgrade material on deformation behavior of the GCL were analyzed by using finite element method (FEM) and a relation between the deformations and failure of the GCL was established by comparing the results with those obtained from an experimental study. Based upon these results, recommendations for the use of GCL as a barrier over coarse materials are given.