Nafion, an amphiphilic polymer based on fluorocarbon backbones and acid groups, is probably the most widely used fuel cell membranes. According to its hydration level it self-organizes leading to nano-cavities through which water diffuse. The diffusion of water that controls the protonic transport is then central in the conversion of chemical energy to the electrical one. Recently, a sub-diffusive and heterogeneous dynamics of water were experimentally evidenced paving the way for more efficient fuel cell membranes. Fundamentally, this dynamics which occurs at the nanoscale needs to be microscopically understood. Molecular dynamics simulations are thus performed to locally examine the water dynamics and its relation with the water and Nafion structure. The sub-diffusive regime is numerically corroborated and two sub-diffusive to diffusive transitions are found. The first is time dependent whereas the second is rather water uptake dependent. The sub-diffusive regime is ascribed to the water molecules strongly anchored close to the acid groups. We show that the sub-diffusive to diffusive time transition is the result of the elapsed time before to escape from the attractive interactions of the acid groups. The diffusive regime is recovered far from the acid groups in a homogeneous water phase that is the result of the percolation of the hydrogen bonding network. The progressive transition between sub-diffusive to diffusive regime as a function of the hydration level is due to the respective weight of diffusive dynamics that increases with respect to the sub-diffusive regime given the increase in diffusive pathways as the expense of the localized dynamics. Close to the fluorocarbon backbones the dynamics of water is also sub-diffusive but faster whereas time dynamical transition is not observed. Furthermore we highlight the existence of water corridors based on the hydrogen bonds between molecules forming single file structure in line with a sub-diffusive dynamics. These water corridors are thus possible conducting pathways of protons in a Grotthuss mechanism. Structurally we depict an interdigitated structure where the sulfonate are interleaved. Eventually, at high water uptake, we exhibit the self-organizing of Nafion leading to a phase separation between water and the Nafion membrane. We establish a specific interfacial organization of the hydrophilic sulfonate groups involving a water/Nafion interface.