The role of fluoropolymer physicochemical properties in the dynamic evolution of nanostructure and ionic conductivity in perfluorinated sulfonic acid ionomer thin films was investigated by in situ water sorption experiments. The properties and mass fraction of the ionomer matrix were systematically varied between Nafion and a perfluorodioxolane ionomer with the same sulfonic acid side chain and mass fractions ranging from 0.26 to 0.57. Swelling rate constants attributed to Fickian mass transport (∼10–2 s–1) decreased with increasing ionic strength and humidity (i.e., with increased swelling) while rate constants associated with morphological rearrangement (∼10–3 s–1) increased. The rate of deformation, in nm s–1, was primarily dictated by the matrix segmental mobility. Transient hydration-driven conductivity exhibited a single rate constant (∼10–3 s–1) corresponding to the morphological process. In situ grazing incidence X-ray scattering experiments reveal a rapid formation of ionomer domains during Fickian water sorption, followed by a slower ordering of these domains during hydration. This relationship between the rates of swelling and morphological changes confirm/pinpoint transient changes controlling ion conduction mechanisms in ionomer thin films.