Contamination of ion from cathode air on the membrane and electrode assembly (MEA) is the serious degradation source in proton exchange membrane fuel cells (PEMFC). In this study, concentration of ions in air at industry region, street and seaside were measured. There were comparably high concentration of Na+, K+, Ca2+ and Fe3+ in this regions. This paper shows the effects of MEA contamination by these ions generated from humidification water. After 170 hours of fuel cell operation using city water as humidification water, the performance of unit cell decrease to 11% of initial performance. The electrolyte membrane easily absorbed foreign contaminant cations due to the stronger affinity of foreign cations with the sulfonic acid group compared to H+. The contaminant ions existing in the interface between the platinum catalyst and ionomer layer turn out to be the most serious factor to decrease cell performance.