Molecular dynamics computer simulations of water/Nafion mixtures using an all-atom model were performed as a function of temperature and humidity. The simulations are aimed at investigating processes and structures on the picosecond to nanosecond time scale in the nano-phase-separated material with its technological relevance for low temperature fuel cells. Characteristic differences in aqueous pore structure were observed for systems whose water content was varied between 5 and 10 molecules per acid group in the polymer. As expected, proton transport increases significantly with increasing humidity, its mechanism is dominated by the Grotthus structural diffusion mechanism in accordance with earlier studies in simplified model pores. On the simulated time scale no unambiguous conclusions on the role of polymer dynamics for the transport in dry membranes can be drawn.