Polymer electrolyte membrane (PEM) fuel cells have the potential to replace petroleum-based fuels with more environmentally friendly energy sources in transportation and stationary residential applications. Nafion, the dominant PEM material, self-assembles into hydrophobic regions and hydrophilic channels decorated with SO3- that conduct protons via a water mediated mechanism. Structural proton diffusion is expected to dominate, but is hindered upon loss of water. Mono-, di-, and tetra- hydrate trifluoromethanesulfonic acids provide a model system to study proton transport as a function of hydration. Ab initio molecular dynamics reveal stable defect structures, SO3- - H+ interactions, and proton conduction pathways. Results will be compared to path integral molecular dynamics calculations.