Reported results of coarse-grained molecular dynamics simulations rationalize the effect of water on the phase-segregated morphology of Nafion ionomers. We analyzed density maps and radial distribution functions and correlated them with domain structures, distributions of protogenic side chains, and water transport properties. The mesoscopic structures exhibit spongelike morphologies. Hydrophilic domains of water, protons, and anionic side chains form a random three-dimensional network, which is embedded in a matrix of hydrophobic backbone aggregates. Sizes of hydrophilic domains increase from 1 to 3 nm upon water uptake. At low water content, hydrophilic domains are roughly spherical and poorly connected. At higher water content, they convert into elongated cylindrical shapes with high connectivity. Further structural analysis provides a reasonable estimate of the percolation threshold. Radial distribution functions from coarse-grained and atomistic molecular dynamics models exhibit a good agreement. Water cluster size distributions from coarse-grained molecular dynamics and dissipative particle dynamics are consistent with small angle x-ray scattering data. Moreover, we calculated the water diffusivity by molecular dynamics methods and corroborated the results by comparison with pulsed field gradient NMR.