Anion-conductive ionomers are used for electrolyte membranes in membrane-electrode assemblies and for binders in catalyst layers in anion exchange membrane fuel cells (AEMFCs). The conformations of these ionomers as well as their water distribution are important for designing new efficient/durable anion-conductive ionomers for AEMFCs. For a deeper understanding of the distribution of deuterium oxide (D2O) as a function of depth, neutron reflectometry (NR) was carried out on thin films of an anion exchange ionomer, BAF-QAF, with a thickness of approximately 60 nm formed on a thermally formed SiO2 film on Si(100) and on a 20 nm Pt layer deposited on the SiO2 film at a temperature of 60 °C and relative humidities of 0, 50, 70, and 90%. Clear NR modulation was obtained under each condition. The NR data were fit very well with a three-sublayered model parallel to the substrate with different densities of BAF-QAF and D2O. The influence of the SiO2 and Pt substrates was observed not only at the BAF-QAF/substrate interface but also on the entire thin film. The D2O absorption/desorption behavior in each sublayer differed in the BAF-QAF films cast on SiO2 and Pt. The BAF-QAF/SiO2 interface was rather hydrophilic, while the BAF-QAF/Pt interface was very hydrophobic.