Toward an enhanced water-retention of polymer electrolyte membranes at high temperatures, novel organo-modified clays were prepared and tested as fillers for the creation of hybrid Nafion nanocomposites. Two smectite clays (Laponite and montmorillonite), with different structural and physical parameters, were loaded with various cationic organic molecules bearing several hydrophilic functional groups (-NH(2), -OH, -SO(3)H) and incorporated in Nafion by solution intercalation. The resulted hybrid membranes were characterized by a combination of powder X-ray diffraction, FTIR spectroscopy, and thermal analysis (DTA/TGA) showing that highly homogeneous exfoliated nanocomposites were created where the individual organoclay layers are uniformly dispersed in the continuous polymeric matrix. In this paper, water-transport properties were investigated by NMR spectroscopy, including pulsed-field-gradient spin-echo diffusion and spectral measurements conducted under variable temperature. Organo-montmorillonite nanofillers demonstrate a considerable effect on the Nafion polymer in terms both of water absorption/retention and water mobility with a remarkable behavior in the region of high temperatures (100-130 °C), denoting that the surface modifications of this clay with acid organic molecules significantly improve the performance of the final composite membrane. (1)H NMR spectral analysis allowed a general description of the water distribution in the system and an estimation of the number of water molecules involved in the hydration shell of the sulfonic groups as well as that absorbed on the organoclay particles.