Polyelectrolyte membranes (PEM) such as Nafion (Du Pont) used as compartment separators in fuel cells and other electro-chemical applications are also of interest as permselective diffusion barriers in protective fabrics. By means of sorption and permeation experiments in conjunction with molecular dynamics simulations, we explore the permeability of Nafion membrane to water and hydrophilic solvents such as 1-propanol and dimethyl methylphosphonate, focusing on the relationship between polymer structure, solvation, and solvent diffusion. It is shown that the composition of the solvent strongly affects the membrane permeability, which cannot be predicted purely from permeability measurements with pure components. This effect is related to a complex microphase segregation in the membranes swollen in aqueous solutions of polar solvents. The results obtained demonstrate possible mechanisms of the diffusion of alcohols and alkyl-phosphonates in hydrated ionomer membranes and reveal properties controlling the utilization of PEM for protective fabrics.