A rationalized study about perfluoronated sulfonic acids based (PFSA) membranes is reported using molecular dynamics simulations. PFSA membranes are a wide used class of materials in proton exchange membranes as solid-electrolytes. Those materials self-organize upon hydration leading to a segregated hydrated nanostructure governing water dynamics and conduction properties. Two commercial membranes, namely Nafion and Aquivion are simulated. The impact of the chemical nature and hydration state on nanostructure and confined water dynamics are both explored. We find that the local nanostructure, depicted by the size of water domains dw and percolation state, and dynamical properties are both irrespective of the side chain length and spacing of the simulated membranes. A transition between a non-percolated water network to a percolated one is evidenced as water content increases and is strongly correlated with water dynamics properties. We find both structural and dynamics properties to be directly dependent on the water volume fraction φw. This study finally points out that the water volume fraction is a key-parameter governing structure/properties relationships in PFSA membranes.