Polymer electrolyte membranes (PEMs) are representative systems for the study of the proton conduction mechanism and water dynamics in nanopores/channels. Our 1H nuclear magnetic resonance data for Nafion PEMs, which are subjected to thermal degradation and then swollen in water, indicate that (1) water is present next to the side chains even after the removal of the SO3H groups, (2) longer heat-treatment depletes more SO3H groups and produces more CF2H groups, (3) the water near the side chains allows for the liquid-like motion of the CF2H groups, and (4) the motion correlates well with the content and dynamics of water in the channels. As the thermal degradation progresses, the Nafion membranes lose their ionic and hydrophilic nature due to the conversion of CF2SO3H groups to CF2H groups. In addition, our results demonstrate that increasing channel hydrophobicity leads to increased water dynamics in the channels.