We used classical molecular dynamics simulation with the DREIDING force field to characterize the changes in the nanostructure of Nafion membrane brought about by systematically changing the hydration level. We calculated the relative percentages of free, weakly bound, and bound water in hydrated Nafion membranes. At low hydration levels, coordination of hydronium ions by multiple sulfonate groups prevents vehicular transport and impedes structural transport of protons through steric hindrance to hydration of the hydronium ions. Our results provide insights into the nanostructure of hydrated Nafion membrane and are in excellent agreement with experimental observations by neutron scattering of changes in the percentage of non diffusing hydrogen atoms.