Polymer electrolyte fuel cells are an essential technology for future local emission-free mobility. One of the critical challenges for thriving commercialization is water management in the cells. We propose small- and wide-angle X-ray scattering as a suitable diagnostic tool to quantify the liquid saturation in the catalyst layer and determine the hydration of the ion-conducting membrane in real operating conditions. The challenges that may occur in operando data collection are described in detail-separation of the anode and cathode, cell alignment to the beam, X-ray radiation damage, and the possibility of membrane swelling. A synergistic development of experimental setup, data acquisition, and data interpretation circumvents the major challenges and leads to practical and reliable insights.