Water and methanol transport properties through bare recast Nafion and composite Nafion membranes containing ceramic fillers characterised by different acid–base behaviour were investigated by nuclear magnetic resonance (NMR) spectroscopy. The water self-diffusion coefficients were determined for the different membranes in the temperature range from 25 to 150°C; the methanol self-diffusion coefficients were recorded for the most performing composite membrane (Nafion–SiO2) and compared to the bare Nafion membrane. Water and methanol transport characteristics of these membranes were correlated to the electrochemical behaviour in direct methanol fuel cells. NMR and electrochemical polarization data indicate that both electrical properties and transport mechanism are influenced by the surface properties of the inorganic fillers; there is a clear evidence that acidic fillers such as silica promote the proton transport in the membrane with respect to basic alumina.