The perfluorinated sulfonic acid membrane (Nafion) shows among ionomers high water uptake and cationic conductivity. These properties allow Nafion to be used in nanocomposite actuators, sensors and fuel cells. In situ experiments have shown that there is a water gradient within the Nafion membrane. The water gradient causes the alteration of other physical properties within the thickness of the membrane and has a drastic impact on the performance of the devices made of the Nafion membrane. Deriving closed-form equations and using molecular dynamics (MD) simulation results, we bridge Nafion properties at the atomic scale and the macroscopic behavior of the membrane within a hierarchical multi-scale model. Multiple discrete simulation cells are selected across the thickness of the membrane with a wide range of water contents as representative volume elements (RVEs). The present framework is able to quantitatively predict the macroscopic properties of Nafion with the nanometric resolution regarding the water gradient across the membrane.