—The molecular aggregation of organic dyes onto clay mineral particles is a very complex phenomenon including dye adsorption, the migration of dye molecules, rearrangement of initially formed aggregates, etc. Some details of this complex process are not yet fully understood. The objective of the present study was to understand the influence of dye surface concentration on the dynamic processes in dye molecular aggregation. A stopped-flow rapid mixing device was used for accurate measurements of the molecular aggregation of the cationic dye rhodamine 123 (R123) in montmorillonite (MntK) colloidal dispersions. The influence of dye surface concentration, which was changed by altering the ratio of the amount of R123 to the mass of MntK (nR123/mMntK), was examined in detail. Chemometric analysis was used to reconstruct the spectral matrix to obtain linearly uncorrelated spectral profiles of the major components and their concentrations at the respective reaction times. The conversion of isolated R123 cations into oblique J-aggregates (head-to-tail molecular assemblies) was observed over time and the existence of a J-dimers intermediate was hypothesized. The reaction kinetics followed a biphasic exponential function. An unexpected effect of dye surface concentration on R123 aggregation was observed: the initial formation of the molecular aggregates increased significantly with dye surface concentration, but an inverse trend was observed after longer reaction times. While dye aggregates were formed slowly at low dye loadings, systems with high R123/MntK ratios (nR123/mMntK) reached spectral stability after the first few seconds of the reaction. After longer reaction times, the greatest degree of dye aggregation was achieved in the dispersion of the lowest dye loading. Such a phenomenon is described for the first time. The results presented here are important for understanding the complex processes occurring in systems based on organic cations and clay minerals, and should be considered in the development of functional hybrid materials of dyes and nanoparticles with a layered structure.