Water management and flooding play an important role in the performance and durability of polymer electrolyte fuel cells (PEFCs). In this study, a dynamic electro-mechanical analysis is performed to examine the performance of a working PEFC during hydration transients and flooding events. Cell resistance is measured using electrochemical impedance spectroscopy (EIS), and the stress/strain characteristics – cell compression and membrane electrode assembly (MEA) dimensional change – are studied using a controlled compression unit (CCU).Ex-situ measurements of membrane thickness as a function of hydration level provide a direct correlation between ionic conductivity and thickness. During initial hydration of Nafion membranes there is a direct relationship between membrane conductivity and dimensional change (swelling) of MEAs. Electrode flooding is found to result in membrane hydration and an increase in stress or strain, depending on the compression mode of the fuel cell. Results suggest that hydration cycles and flooding events can lead to cell degradation due to the stresses imposed.