In-situ fluorescence experiments were performed with 6-carboxy fluorescein (6CFL) as the fluorescent molecular probe for monitoring reactive oxygen species (ROS) formation in an operating fuel cell. Modified rhodamine 6G (R6G) was used to prevent platinum-6CFL interactions (metal-dye interactions) during these measurements. ROS generated during fuel cell operation degrade the Nafion® membrane resulting in the release of fluoride ions. The concentration of fluoride was measured ex-situ in the effluent stream at regular time intervals and the trend of the ex-situ fluoride-ion concentration data mirrored the trend of the in-situ fluorescence data. The effect of relative humidity on ROS induced degradation was examined with the in-situ and ex-situ techniques. Lower relative humidities resulted in greater ROS induced degradation. Additionally, we report the modification of cerium (IV) oxide with doped nitrogen resulted in a sustained efficacy for free radical scavenging.