Synchrotron radiation (SR) based imaging of polymer electrolyte fuel cells (PEFC), both radiography and tomography, is an attractive tool for the visualization of water in the gas diffusion layer as it provides temporal and spatial resolutions one order of magnitude superior to neutron imaging. Here we report on the degradation of cell performance and changes in GDL water saturation after SR irradiation of about 43% of a cell's active area. Fast X-ray tomographic microscopy (XTM) scans of 11 s duration are used to compare the GDL saturation before and after a 5 min irradiation period of the imaged section. The cell voltage and the water saturation decreased clearly during and after the exposure. Estimates of the current density of the SR exposed and non exposed cell domains underline the effect of irradiation.