Polymer-catalyst interfaces control the energy efficiency of many energy conversion and storage device. The interfacial polymer layers are very thin (typically less than one micron thick). Many interesting structural, mechanical and transport properties in such thin ion containing polymer (ionomer) layers evolve as a result of complex multimodal interfacial interactions, unusual hydration behavior and confinement. Especially ion conductivity at the interface can be drastically different from that in the bulk membranes and the route to this poor ion conduction behavior is not well-understood. It is thus highly needed to systematically study how the ion conduction environment and water uptake change with the change in ionomer structure and film thickness. In this work, three potential fluorocarbon based hydrogen fuel cell ionomers (Nafion, 3M PFIA, 3M PFSA) having single/multiple acids at side chain were studied in sub-micron thick films. All three ionomers have fluorocarbon (PTFE) backbones. The difference between Nafion and 3M PFSA is in the side chain structure, but both has single acid group at the side chains. On the other hand, 3M PFIA has bis(sulfonyl)imide group in addition to perfluorosulfonic acid which makes the polymer more acidic. By tracking the fluorescence response of photoacid dye HPTS incorporated within hydrated ionomer thin films, very interesting trends were obtained regarding the extent of proton transfer. The results, when combined with the information on nanoscale structure and water sorption, clearly indicated that there are many factors controlling the proton conduction behavior in thin ionomer films, in addition to water uptake.