Perfluorosulfonic acid (PFSA) polymer electrolyte membranes like Dow, Aciplex and Nafion have similar backbones but different side chain pendants. The effect of hydration and temperature on the side chain pendant nanostructure, and water and hydronium ion dynamics, are investigated by employing classical molecular dynamics simulations at 300 K and 350 K. The 60% longer side chain pendant length in Aciplex compared to Dow results in phase segregation. The presence of an extra ether oxygen atom in the Nafion side chain pendant provides more flexibility ($20% chain length contraction caused by flexibility and the hydrophobic force of the pendant CF 3 group) where the sulfonate group tends to drift from the hydrophilic-hydrophobic domain, which gives rise to a hydrosphere region at higher hydration.The calculated structure factors and scattering intensities reproduce features of SANS and SAXS profiles for Dow and Nafion, and confirm the existence of spherical water aggregates in the rod shaped pendant nanostructure of Nafion. The effect of hydration on the mobility of hydronium ions at 300 K in Nafion is insignificant at higher hydration (l $ 9), and trends are in agreement with experimental data. The activation energy of the diffusion of hydronium ions and water molecules in Nafion side chain pendantwater mixtures (14-25 kJ mol À1 ) validate experimental observations (16-22 kJ mol À1 ). Fig. 1 Chemical structure of PFSA polymer membranes (ionomer form).