Degradation of proton exchange membrane fuel cells (PEMFCs) can be accelerated by impurities in the air. In maritime environments in particular, sodium chloride (NaCl) can reduce the performance of membrane electrode assembly (MEA) in PEMFCs. In this context, we experimentally analyzed effect of flow channel depth on PEMFCs humidified with a NaCl solution at the cathode side. The analysis was conducted in serpentine flow channels with different depths of 0.4, 0.8, and 1.6 mm. The initial performance of unit cells was compared to their performance after applying a constant current for 10 hours. Results showed that the degradation rate correlated positively with the flow-channel depth. Channel depths of 0.4 and 1.6 mm resulted in 2.4% and 7.3% decreases in the maximum power density, respectively. For the 1.6 mm channel depth, the activation loss after 10 hours was larger than the initial loss.