Structures of perfluorinated polymer membranes in dry and wet state and their molecular dynamics have been studied by Neutron Small Angle Scattering and Neutron Spin Echo. In swolen membranes there were observed proton conducting channels (~ 1-2 nm in diameter) being branched fractals (dimension ~ 2.2-2.6). In these structures, in the experimental time-interval t = 0-150 ps, the detected fast dynamics reflected mainly water diffusion mixed with protons’ hopping from one water molecule to another during proton exchange between ionic groups SO3H in side chains of macromolecules. To reinforce the channels’ system and proton conductivity, the membranes’ modification was developed by embedding nanodiamonds with hydrophilic surface since in aqueous solutions they create gel networks with the cells of ~ 40 nm in size. In composite membranes a dopation with nanodiamons (size ~ 4-5 nm, concentration ≤ 1 % wt.) has stimulated proton conductivity at the enhanced temparatures (20-50oC).