In this study, the change of electrochemical parameters during the gradual water accumulation of a polymer electrolyte fuel cell (PEFC) are estimated using electrochemical impedance spectroscopy (EIS) measurements and an impedance model based on electrode theory during a two‐step oxygen reduction reaction (ORR). EIS measurements were carried out in a 5 cm2 H2/O2 PEFC operated under a dead‐ended configuration of the gas reactants and during gradual accumulation of water. Kramers‐Kronig evaluation demonstrated that the EIS measurements comply with stability and linearity properties and the inductive loops featured at low frequencies are attributed to electrochemical mechanisms within the PEFC and not to instability during gradual water accumulation. The impedance model has been reported in a previous study and simulates inductive loops at low frequencies which are attributed to platinum oxide formation during the ORR. The estimated parameters obtained from this EIS‐modeling analysis can provide an insight into the decrease in PEFC performance during flooding conditions. A further qualitative analysis considering the effect of long‐term water accumulation on the oxygen‐reduction charge transfer resistance is discussed. It is possible to have an insight into the physical mechanisms of the PEFC, by combining different experimental techniques and fundamental theory in a complimentary manner.