The Nafion membranes are widely used in electrochemical applications such as fuel cells, chlor-alkali cells, and actuators-sensors. In this work, the thermal-optical characterization of Nafion in acid form was performed by photoacoustic spectroscopy, thermogravimetry, and differential scanning calorimetry. In the experimental procedure three distinct hydration levels were considered: (1) pristine membrane (λ ≅ HO/-SOH ≅ 5.6); (2) swelling process (λ ≅ 17.4); and (3) drying at controlled room temperature after swelling process (λ ≅ 6.5). The discovered behaviors showed significant irreversible structural changes induced by water retention in the membrane. These structural changes depend on the water population present in the clusters and also affect the directional thermal diffusivity of the membrane irreversibly.