The employment of clay minerals in the transport of water, nutrients, and contaminants depends on a few factors, including permeability, hydration behavior, ion-exchange efficiency, and more. With the application of external stress, it is still difficult to understand how clay particles swell and collapse, how water is retained, how hydration heterogeneities are formed within crystallites, and how interlamellar space is organized. The present work studied the link between geochemical, thermal, kinetic constraints (established at the laboratory scale), and intrinsic clay features by exchanging Na-rich montmorillonite (SWy2) with Ni2+, Mg2+, or Zn2+ cations. By comparing the experimental 00l reflections with the calculated reflections obtained from the structural models, quantitative X-ray diffraction (XRD) analysis has enabled the building of a theoretical profile describing the layer stacking mode (LSM) and allowed the description of interlayer space (IS) configuration along the c* axis. Regardless of the type of the exchangeable cations (EC), XRD modeling revealed that all samples exhibited interstratified hydration behavior within the crystallite size, which probably indicates partial or incomplete saturation of the IS. This theoretical result was defined by the appearance of two hydration states (1W and 2W), which were unrelated to the strain strength creating a higher degree of structural heterogeneity. Using the theoretical decomposition of the observed XRD patterns, the identification of all distinct layer populations and their stacking mode was achieved. The segregated LSM are, therefore, obviously superior as a function of stress strength.