The microstructural changes associated with the lowering of hydrophilic/hydrophobic phase separation in the ionomer can reduce the molecular permeation without compensating the ionic conductivity significantly. Motivated by this idea, a hydrophilic polymer, poly(vinyl alcohol) (PVA) was selected as the polymer matrix of the proton exchange membranes and the protogenic sulfonic acid groups were introduced by chlorosulfonic acid through a condensation reaction. Glutaraldehyde was used as the cross-linking agent to improve both the mechanical and thermal stabilities of the membrane. The chemical structure and microstructural features of the membranes have been analyzed using FTIR-ATR and DSC, respectively. The different states of water in the membranes were analyzed and the role of nonfreezing water in the selective transport is discussed.