Epoxy nanocomposites with commercially and self-modified montmorillonites of different cation exchange capacities carrying ammonium modifications of various chemical architectures were synthesized using solution casting approach. The commercially treated montmorillonites were observed to contain a large excess of unbound ammonium ions on the surface, which had a negative impact on the permeation properties of the composites owing to the suspected interactions of these unbound ammonium ions with the epoxy polymer. The permeation behavior was significantly improved when self-modified clays free of any excess ammonium modification were used. The microstructure development was unaffected by the physical state of the clay surface indicating that the potential changes in the polymer properties at the interface as well as interfacial interactions in the composites carrying the commercially modified clays may have led to increase in the free volume. Optimal preparation of the clay surface holds the key to achieve enhancement in the composite performance.