A fluorescence spectroscopy system has been set up for studying the interaction of molecular probes (fluorescent dyes) with hydroxy and hydroperoxy radicals. From this work, a method will be developed for in-directly monitoring the chemical degradation of the Nafion® membrane in-situ during fuel cell operation. Different molecular probes (Fluorescein and 6-carboxy Fluorescein) have had their fluorescence signal assessed in solvent environments of varying pH. Stern-Volmer relationships have been observed and fitted to correlate hydrogen peroxide concentration to fluorescent signal quenching. Additionally, free radical scavengers were added to formulations and have shown to mitigate the free radical attack on the molecular probe.