Thermally induced changes in surface wettability, dewetting behavior, and proton transport of "self-assembled" nanothin Nafion (R) films (4-300 nm) on SiO2 substrate is reported. Thermal annealing induces switching of the surface wettability of 55 nm and thinner films from hydrophilic to super-hydrophobic. Thickness dependence of this behavior is observed with higher annealing temperature required for lower thickness films, indicating highly restrictive mobility of Nafion (R) ionomer as film thickness decreases. Dewetting is only observed for 4-nm thin film. Significant suppression in proton conductivity upon thermal annealing was noted. Similarly, two other bulk properties, water uptake and swelling, were found to decrease upon annealing. This work reports a systematic examination of the thickness dependence of thermally induced changes in both surface and bulk properties of ultra-thin Nafion (R). (C) 2016 Wiley Periodicals, Inc.