The phase transition behavior of water in the perfluorosulfonate ionomer membrane, Nafion, was investigated using a differential scanning calorimeter (DSC). The equivalent weight of the membrane used was 1.100 g/eq.. Three kinds of alkali ions, ammonium ion and four kinds of alkyl ammonium ions were used as the membrane counter ion. Water molecules in the membranes were classified into three types, non-freezing, freezing bound and free water. From the heat of crystallization, the amount of each type of water was determined. The number of non-freezing water and freezing bound water per ion exchange site was calculated from the equilibrium amounts of each type water. The number of non-freezing and freezing bound water molecules per ion exchange site, which increased with increasing number of methyl groups of the alkyl ammonium ion, corresponds well with the permeate flux and the selectivity of water in the case of the alkyl ammonium ion series. The permeate flux decreased and the selectivity increased with increasing interaction between water molecules and alkyl ammonium ions. For the alkali ion series, the opposite relationship was observed between permeate flux, selectivity and number of non-freezing water per each ion, because the ionic cluster-size swelling with water determined the permeate behavior.