PFSA-based reinforced membranes are used today as the benchmark material for the electrolyte in PEMFCs. Although greatly improved relatively to their unreinforced version, they still suffer from aging and degradation during fuel cell (FC) operation. In this study we first performed proton NMR to characterize the different water populations in the pristine Nafion XL reinforced membrane. Then we used proton and fluorine NMR, FTIR and sorption measurements in order to qualitatively observe the differences induced in the membrane’s chemical structure and properties by long term FC operation. Proton NMR is seen to be an adapted tool to quickly measure a signature that is correlated to the degradation state while FTIR can serve as a local probe of the chemical structure.