Polymer electrolyte fuel cells (PEFCs) for marine vessels have been expected to reduce the pollutant emissions on the sea. Since marine PEFCs operate under harsh conditions, such as ship vibrations and sea salt exposure, the diagnosis of abnormal operational conditions is of a great importance to improve the reliability and durability of PEFCs in marine power application. Electrochemical impedance spectroscopy (EIS) is a technique suitable for real-time diagnosis of PEFCs in operation. In the present study, EIS was used to assess the factors to determine the performance of PEFCs, namely operating temperatures, cathode fed air conditions of relative humidity, flow rates and sea salt (NaCl) contamination. EIS spectra were obtained through Fast Fourier Transform (FFT) EIS techniques, while a transmission line model (TML) with the ohmic resistance of the ionomer was used as an equivalent circuit for the analysis. Under conditions of dehydration (dry-up), we observed an increase in the ionomer/electrolyte membrane ohmic resistances and the charge transfer resistance. When liquid water was excessive (flooding), mass transfer resistance drastically increased in the cathode. All resistance also increased after NaCl solution was injected into the cathode inlet. In particular, charge and mass transfer resistances were the main factors that led to an increase in the polarization loss. Injecting distilled water after detecting NaCl contamination at an earlier stage is effective to mitigate irreversible degradation.