We report on a computational project investigating the transport of protons across the electrode/electrolyte interface of hydrogen PEM fuel cells. Our molecular simulations of the bulk hydrated membrane show a morphology of the aqueous nanophase within the system that loses connectivity at low humidity, leading to a drop in vehicular diffusion of protons. Structural analysis of the degree of hydration of protons indicates a drop in structural diffusion as well at low humidity. At the membrane/vapor interface, we observe a slightly dehydrated region that will negatively impact both the vehicular and structural components of the hydronium diffusivity. At the membrane/vapor/electrode support interface, we do not observe any wetting of the electrode support surface. At the membrane/vapor/catalyst interface, we observe significant wetting of the catalyst surface by a mixture of water and polyelectrolyte. Taken as a whole, this data suggests that the placement of catalyst particles and the degree of humidity is crucial to optimizing the proton transport across the electrode/electrolyte interface. We draw connections between our molecular-level understanding and implications for fuel cell nanostructured design. Finally, we report on a new, generalizable model for structural diffusion of protons in molecular dynamics simulations.