The microphase segregation in the Nafion (DuPont trademark) perfluorinated membrane at different water contents was studied using molecular dynamics simulations. As the degree of solvation increased, we observed the formation of water clusters containing up to ca. 100 water molecules. In contrast to the conventional network models, the water clusters do not form a continuous hydrophilic subphase. The cluster size distribution is rather wide and evolves in time due to formation and break-up of temporary bridges between the clusters. This dynamic behavior of the cluster system allows for the macroscopic transfer of water and counterion. The calculated diffusion coefficients of water were found to be on the same order as the experimental ones.