Nafion 212 membrane was subjected to swelling–dehydration (SD) cycles, as a relevant operation condition for direct methanol fuel cells (DMFCs). The major degradation mechanism due to the treatment was found to be sulfonic group contamination with trace ion, rather than formation of sulfonic anhydride, which is a well-known degradation mechanism for Nafion® membranes under hydrothermal (HT) aging condition. The consequences of the degradation include decreasing water content, thickness, and surface fluoride and increasing resistance, dry weight, and a changed surface morphology. Ion selectivity of the sulfonic group was studied toward different fuel cell relevant conditions. It turned out that the sulfonic groups have much higher selectivity toward cations rather than neighbor sulfonic groups. Trace impurities in the liquid methanol feed in DMFC may therefore represent an important contamination source.