Neutron studies of the channels for molecular and ionic transports in membranes modified with different nanoparticles were carried out. In the polyphenylene oxide film modified with polymers composed of fullerene with grafted with polystyrene and poly-2-vinylpyridine arms, the formation of linear channels for diffusion at the modifier–matrix interfaces was detected. In the membranes of perfluorinated copolymers with SO3H ionic groups, embedded detonation nanodiamonds induced the expansion of the channels for better proton conductivity. The discovered subtle mechanisms of membranes structuring by different modifiers are relevant for advanced membrane design.