In this work, we elucidated the nanostructure and dynamics of Nafion-doped graphene-oxide (GO) systems from molecular dynamics simulations at varying hydration levels and temperature. It was found that the presence of GO resulted in the formation of Nafion layers along a direction normal to the GO surface. Chain conformations in the Nafion layers close to the GO interface were characterized by a backbone preferably oriented parallel to the GO plane, whereas the size of the formed nanochannels was found to be commensurate to the average dimensions of the Nafion side chains. The mechanism of water cluster growth was found to change drastically upon introduction of Nafion chains, although addition of GO in the membranes did not impart further measurable changes at the examined temperatures. Hydronium ions were found to adsorb partly onto the GO surface, whereas the pertinent adsorption/desorption rate increased significantly with hydration. Translational dynamics of water molecules was much slower close to the GO surface compared to that at distances far from GO. In the temperature range examined, the dynamics of the effectively confined water molecules was found to follow an Arrhenius-like dependence. Water retention at the Nafion/GO interface appears only at high hydration levels of Nafion.