Engineering of clay nanocomposite materials by modification of their surfaces can enable the control of retention, transport, and persistence of toxic chemicals in the geosystem. The properties and interactions of clay nanocomposites have been widely studied, but little information exists on their microstructure at a range of scale extending down to atomic dimensions. The pairing of Na-montmorillonite clay with organic cations as well as with the herbicide fluridone, chosen as a model for an organic pollutant, was studied. Three organic cations were selected: hexadecyltrimethylammonium, benzyltrimethylammonium, and benzyltriethylammonium at 0%, 60%, and 100% of cation exchange capacity (CEC) loadings. A detailed microstructural analysis of the organo-clay nanocomposites and of the fluridone nanocomposites was undertaken by high-resolution transmission electron microscopy (HRTEM) and X-ray energy-dispersive spectroscopy (EDS). Morphological observations and chemical analyses were performed simultaneously on the same sample. The combined HRTEM and EDS measurements strongly suggest (a) heterogeneous local intercalation of the organic cations manifested by a range in the measured d001 spacing, implying random expansion of the clay layered structure with increased loading of the organic cations; (b) intercalation within the external layers, which is thoroughly influenced by local defect microstructure and/or edge availability of the montmorillonite nanoparticles as well as by the molecular structure of the intercalating organic cation. Additional intercalation of fluridone molecules did not affect the structure (d001 spacing) of the organo-clay nanocomposites.