Molecular Dynamics (MD) techniques have been used to study the structure and dynamics of hydrated Li- and Na-Nafion membranes. The membranes were generated using a Monte Carlo-approach for Nafion 117 oligomers of Mw = 1100 and with water contents of 7.5 and 20 % by weight, equivalent to 5 and 15 water molecules per sulfonate group, respectively. After equilibration, local structural properties and dynamical features such as coordination, cluster stability, solvation and ion conductivity were studied. In a comparison between the two cationic systems, it is shown that the Na-Nafion system is more sensitive than Li-Nafion to the level of hydration, and also show higher ion conductivity. The ionic conductivity is shown to increase with higher level of hydration.