Small angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) investigations of recast composite and bare Nafion membranes have been carried out. The self-diffusion coefficients of water and methanol have been determined over a wide temperature range by PFGSE 1H NMR method. The transport mechanism appears to be influenced by surface properties of inorganic fillers. Acidic silica filler appears to promote proton transport in the membrane with respect to basic alumina. An interaction of the silica surface with methanol molecules is also envisaged from the analysis of proton self diffusion coefficients of methanol. The SAXS analysis revealed a modification of the polymer structure immersed in pure methanol or methanol solution with respect to water. A significant increase of the average ion clusters dimension is observed for the composite SiO2 membrane.