Significant effort has been invested previously to understand the effect of temperature and humidity on water uptake, water transport, structure, and proton conductivity of perfluorosulfonic acid (PFSA) ionomer membranes. One of the significant factors influencing the performance and durability of Nafion is its ability to retain and transport water. Water transport in Nafion is a strong function of sorption, ion exchange capacity, and transport properties of the membrane, which in turn, are functions of its structure and morphology. In addition to the operating conditions, pre-treatment conditions, additives, and the presence of cations significantly affect Nafion's morphology. Infrared spectroscopy (IR) is a powerful tool to gain insight into the properties of Nafion structure and properties. FTIR can monitor real-time changes in chemical interactions, molecular motions, and connectivity of ionic channels under varying operating conditions. FTIR has also been used to validate models developed to explain the dynamic behavior of polymer electrolyte membrane fuel cells. The potential of infrared spectroscopy to understand the impact of environmental changes on Nafion structure is immense but remains underutilized. This review provides a comprehensive summary of the assignment of vibrational modes of Nafion in various regions of the spectrum and sheds light on discrepancies concerning the allocation of vibrational modes to specific interactions.