Nafion has long been the state-of-the-art solid polymer electrolyte material for a range of next-generation electrochemical energy and chemical separation devices, such as polymer electrolyte membrane fuel cells (PEMFCs). While significant attention over several decades has focused on the polymer structure, proton transport mechanism, and structure-function relationships for bulk membranes, only recently has attention turned to Nafion properties in the catalyst layer (CL), the complex heterogeneous layer where key limiting charge-transfer processes in the PEMFC occur. Recent work suggests that high transport resistance in the CL Nafion contributes to poor PEMFC performance with low Pt loading, but the specific causes of the transport limitations and their implications for PEMFC design are not fully understood. Understanding and quantifying the role of CL Nafion in limiting PEMFC performance is hindered by the complex nano- and micro-structure of the CL – where thin Nafion sheets coat ionomer-flooded agglomerates of carbon-supported Pt catalyst nanoparticles – and by the complex influence of multiple material interfaces and operating conditions on the thin-film Nafion properties. We report here the of dependence of the polymer ionic domain structure and water uptake on the thickness of ultrathin Nafion films (ranging from 5 – 153 nm) coated onto hydrophilic SiO2 substrates, using in situ neutron reflectometry (NR) as a probe. NR is capable of determining structure with sub-Angstrom precision in idealized planar interfaces. Because of isotopic variations in neutron scattering cross sections, it is particularly sensitive to certain elements such as H (and thus water) as well as Li, V, and numerous others. Our results herein show that ionic domains form as sheet-like lamellae at the SiO2 interface, with a thick, bulk-like layer forming at the lamellae/vapor interface for films thicker than 20 nm. The bulk-like layer water uptake increases with increasing thickness for films with equivalent Nafion thickness t Naf < 60 nm, but these bulk-like layers have constant water uptake, similar to bulk 1100 eq. wt. nafion (l = 10) for t Naf ≥ 60 nm. We also show that while the lamellae form due to substrate interactions, their structure and water uptake are also influenced by the presence and composition of the bulk-like layer. Finally, these results indicate that inferring water content from whole-sample measurements (such as swelling or mass uptake measurements) can, in some cases, give an insufficient or even inaccurate measure of the Nafion water uptake. These structural measurements from NR are then used to predict the ionic conductivity of ultrathin Nafion films, using previously established relationships for s ion based on l. Fitting these predictions to experimental data provides evidence of transport limitations in the Nafion film, which increase with increasing proximity to the substrate, and helps to explain previously counter-intuitive trends in ionic conductivity vs. thickness for these films. These effective conductivities are then implemented in numerical simulations of the PEMFC anode and cathode catalyst layers, and demonstrate that both finite thickness effects and sheet-like ionic domain structures at film interfaces can have significant implications for PEMFC performance.