We present a detailed analysis of the nanostructure of the short side chain (SSC) perfluorosulfonic acid membrane and its effect on H2O clustering, H3O+ and H2O diffusion, and mean residence times of H2O near SO3− groups based on molecular dynamics simulations. We studied a range of hydration levels (λ) at temperatures of 300 and 360 K, and compare the results to our findings in the benchmark Nafion® membrane. The water cluster diameter is nearly the same in the two membranes, while the extent of SO3− clustering is more in the SSC membrane. The calculated cluster diameter of about 2.4 nm is in excellent agreement with the recently proposed cylindrical water channel model of these membranes. The diffusion coefficients of H2O and H3O+ are similar in SSC and Nafion membranes. Raising the temperature of the SSC membrane from 300 to 360 K provides a much bigger increase in proton vehicular diffusion coefficient (by a factor of about 4) than changing the side chain length. H3O+ ions are found to exchange more frequently with SO3− partners at the higher temperature. Our key findings are that (a) the hydrophobic–hydrophilic separation in the two membranes is surprisingly similar; (b) at all hydration levels studied, the long side chain of Nafion is bent and is effectively equivalent to a short side chain in terms of extension into the water domain; (c) vehicular proton transport occurs mainly between SO3− groups; and (d) changing the size of the simulation cell does not change the results significantly. The simulations are validated in good agreement with the corresponding experimental values for the simulated membrane density and diffusion coefficients of H2O.