Thin films of ion-conducting polymers are an important area of study due to their function in many electrochemical devices and as analogues for interfacial phenomena that occur in bulk films. In this paper, the properties of Nafion, a prototypical ionomer, are investigated as thin films (4 to 300 nm) on carbon, gold, and platinum substrates that are fabricated using different casting methods and thermal histories. Specifically, water uptake, swelling, and morphology are investigated by quartz-crystal microbalance, ellipsometry, and grazing-incidence X-ray scattering to develop structure/property/ processing relationships. For all substrates, as the films' thickness decreased, there is an initial decrease in swelling followed by a subsequent increase for film thicknesses below approximate to 20 nm due to a disordering of the film hydrophilic/hydrophobic structure. Decreased swelling and less structural order is observed on gold for spin-cast films compared to self-assembled films; the opposite effect is observed for films on carbon. The presented systematic data set and analyses represent a thorough study of the behavior of Nafion thin films on model substrates of interest in metal catalyst/carbon electrodes, and these insights help to elucidate the underlying polymer physics and confinement effects in these and related systems.