A comprehensive study of commercially available and newly synthesized proton conducting perfluorinated sulfonic acid (PFSA) surfactants and polymeric systems is reported, specially designed in a bottom-up search to improve the basic understanding of PFSA polymers used as benchmark electrolytes in fuel cells. Hydration-dependent mesomorphous phases are formed by the self-assembly of these molecules in water. The impact of the hydrophobic chain length, the density of charge, the molecular architecture on the nanostructure, and the dynamics of confined water were studied by combining small-angle X-ray scattering, quasielastic neutron scattering, and pulsed-field gradient NMR. We introduce a hydration-dependent structural parameter, d(w), (mean size of water domains), that allows to establish the structure-transport relationship in PFSA materials. This multiscale study reveals that (i) the dynamical behavior of confined protons and water molecules are rather insensitive to the topology of the host matrix and (ii) the main parameter driving the performance of fuel cell electrolytes is the total water content required for swelling the domains above a value of 1 nm.