Classical molecular dynamics (MD) simulations were performed to determine the hydrated morphology and hydronium ion diffusion coefficients in two different perfluorosulfonic acid (PFSA) membranes as functions of water content. The structural and transport properties of 1143 equivalent weight (EW) Nafion, with its relatively long perfluoroether side chains, are compared to the short-side-chain (SSC) PFSA ionomer at an EW of 977. The separation of the side chains was kept uniform in both ionomers consisting of -(CF2)(15)- units in the backbone, and the degree of hydration was varied from 5 to 20 weight % water. The MD simulations indicated that the distribution of water clusters is more dispersed in the SSC ionorner, which leads to a more connected water-channel network at the low water contents. This suggests that the SSC ionomer may be more inclined to form sample-spanning aqueous domains through which transport of water and protons may occur. The diffusion coefficients for both hydronium ions and water molecules were calculated at hydration levels of 4.4. 6.4, 9.6, and 12.8 H2O/SO3H for each ionorner. When compared to experimental proton diffusion coefficients, this suggests that as the water content is increased the contribution of proton hopping to the overall proton diffusion increases.