Composite membranes based on Nafion with the inclusion of cationic and anionic nanoclays, Laponite, and layered double hydroxide (LDH), respectively, were used to increase the operating temperature of a direct methanol fuel cell (DMFC). The electrochemical behavior of the hybrid nanocomposites was investigated in a single cell at different temperatures (from 90 to 110 °C), and the results were compared with those obtained on the filler-free Nafion membrane. Cell resistance measurements showed a significant improvement of the water retention capability at intermediate temperature for the composite membranes, in particular the LDH-based one. This feature was investigated and explained by a thorough NMR study (diffusometry, relaxometry, and 1H spectral analysis) on the different membranes. Furthermore, the dispersion of 2D plate-like nanolayers in the polymeric matrix demonstrates to be a physical barrier, considerably reducing the methanol mobility through an increase of the tortuosity of the diffusional paths of methanol molecules.