The structure of polymer electrolyte membranes, e.g., Nafion, inside fuel cell catalyst layers has significant impact on the electrochemical activity and transport phenomena that determine cell performance. In those regions, Nafion can be found as an ultrathin film, coating the catalyst and the catalyst support surfaces. The impact of the hydrophilic/hydrophobic character of these surfaces on the structural formation of the films and, in turn, on transport properties has not been sufficiently explored yet. Here, we report classical molecular dynamics simulations of hydrated Nafion thin films in contact with unstructured supports, characterized by their global wetting properties only. We have investigated structure and transport in different regions of the film and found evidence of strongly heterogeneous behavior. We speculate about the implications of our work on experimental and technological activity.