Novel nanostructured organo-modified layered materials based on graphene oxide carrying various hydrophilic functional groups (-NH2, -OH, -SO3H) are prepared and tested as nanofillers for the creation of innovative graphene-based Nafion nanocomposites. The hybrid membranes are characterized by a combination of analytical techniques, which show that highly homogeneous exfoliated nanocomposites are created. The pulsed field gradient NMR technique is used to measure the water self-diffusion coefficients. Remarkable behavior at temperatures up to 140 °C is observed for some composite membranes, thereby verifying the exceptional water retention property of these materials. Dynamic mechanical analysis shows that hybrid membranes are much stiffer and can withstand higher temperatures than pure Nafion.