Diffuse reflectance (DR) spectra in the visible (VIS) and near-infrared (NIR) region of methylene blue (MB) adsorbed on clay samples of different mineral composition and varying MB/clay ratios were analyzed. This type of investigation is not affected by unadsorbed MB molecules and can be used in clay-mineral determination. When the MB dye/clay loading was increased, enhancement of bands in the DR-VIS and DR-NIR was observed. The distribution of various MB aggregates was interpreted according to mineral composition and MB loading. The NIR spectrum of H2O overtone provides insights about the intercalated MB aggregation, consistent with VIS spectra. Critical MB concentration for formation of dimeric structure was between 0.7 and 1.75 mmol/100 g followed with suppression of monomers. Different orientations of vectors of polarized light allowed calculations of the possible orientation and tilting angle of MB molecules on the surface of the clay particles in accordance with XRD data.