The structural, energetic, and mid-infrared spectral properties of water clusters interacting with a model perfluorosulfonate (Nafion) ionomer segment have been investigated by means of quantum chemical calculations. Density functional theory calculations were conducted to model interfacial water condensed in pores and channels of Nafion and helped shedding light on the structural and vibrational properties of hydrated Nafion membranes. The computational models consisted of a sodium counterion, the Nafion ionomer, and a cluster of water molecules positioned in three different regions of the ionomer. The orientations of the water molecules in the vicinity of the ionomer were examined to understand the appearance of O-H stretching bands that deviated from the typical bulk water values as well as the appearance of multiple free O-H stretching bands. The calculations revealed insights into the structure, orientation, and energetics of Nafion and water clusters in and around the membrane interface; the results show that hydrogen atoms at the water-ionomer interface hydrogen bond to the hydrophilic sulfonate group as well as to the hydrophobic fluorinated backbone.