Polymer electrolyte fuel cells are a promising clean alternative to conventional internal combustion engines for transportation applications. Among the issues preventing full-scale commercialization are the high cost of platinum (Pt), transport losses associated with ionomer distribution in the catalyst layer, and management of the water which is produced as a by-product of the fuel cell reaction. The morphology of the catalyst layer plays an important role in the aforementioned challenges. X-ray computed tomography (CT) is an ideal way to study this morphology as it is non-destructive and can resolve structures on both the micro- and nano-scales. Presented here is a novel way to image Pt and ionomer in catalyst layers using cesium staining and x-ray absorption near edge spectroscopy (XANES). Additionally, this work focuses on overcoming barriers in operando hardware design for synchrotron x-ray imaging, focusing on both micro- and nano-scales, which will help explain the interplay between morphology and transport processes, as well as water management. The fuel cells presented here show significant promise, as they can combine the study of electrochemical performance with that of water distribution in fuel cell components during operation.