The presence of water in polymer electrolyte materials has substantial impact on the materials’ morphology, mechanical and transport properties, and thus dedicate the materials' performance in many important applications in energy production and conversion devices such as fuel cells and electrolyzers. In this study, the states and distributions of water in recast H⁺-Nafion^® ionomer films thermally annealed at a temperature up to 120^oC were determined from attenuated total internal reflection FTIR (ATR-FTIR) spectra in the O-H stretching region which were analyzed using principle component and multivariant curve resolution methods. The morphologic changes of the films indicated by the ATR-FTIR experiments are further confirmed by the small-angle X-ray scattering (SAXS) experiments. It is concluded that a Nafion film annealed at a higher temperature results in a more robust polymer matrix surrounding the ionic clusters, and thus exert a stronger restriction on the amount of water uptake in each one of the ionic clusters. The restricted amount of water in the ionic clusters limits the extent of the hydrogen bonding of the water clusters residing in the ionic clusters upon the ionomer film water uptake. These results could lend useful insights on the nature of water in the polymer electrolyte materials, and on the effects of thermal annealing treatment used in fabricating electrodes from the catalyst inks containing the ionomer solution. The impacts of the cathode catalyst layer annealing treatment on the hydrogen/air fuel cell performance are also presented.