The application of polymer electrolyte fuel cells (PEFCs) for marine vessels will be an effective means of reducing the environmental impact and solving energy crisis problems. The diagnosis of abnormal operational conditions is an important aspect of improving the reliability and durability of marine PEFCs, and helps to ensure long-term safe and stable operation. The present work investigates the effect of abnormal variations in the relative humidity of supplied gases on the resistance values in the equivalent circuit model using electrochemical impedance spectroscopy analysis. An appropriate microporous layer coated gas diffusion layer is evaluated to enhance the cell performance under both low and high humidity conditions. The effect of sea salt (NaCI) contamination in the cathode air on the cell performance is also evaluated. Injecting distilled water after the initial detection of performance degradation due to NaCI contamination is effective at recovering the cell performance.