Ion-exchange modeling is used widely to describe and predict ion-adsorption data on clay minerals. Although the model parameters are usually optimized by curve fitting experimental data, this approach does not confirm the identity of the adsorption sites. The purpose of the present study was to extend to divalent cations a previous study on the retention of monovalent cations on Na-saturated montmorillonite (NaMnt) which optimized some of the model parameters using density functional theory (DFT) simulations. The adsorption strength of divalent cations increased in the order Mg2+ < Cd2+ < Ca2+ < Sr2+ < Ba2+. After adding adsorption of metal hydroxide species (MOH+), the three-site ion-exchange model was able to describe adsorption data over a wide pH range (pH 1–10) on NaMnt. X-ray diffraction (XRD) analyses were conducted to investigate the interlayer dimension of clay samples under various conditions. The cation retention strengths of divalent cations did not correlate with interlayer dimensions. The XRD analyses of the Mnt showed a d001 value of 19.6 Å when saturated with alkaline earth cations, 22.1 Å with Cd2+, 15.6 Å with Na+, and 15.2 Å with H+. In the case of Na+, the 15.6 Å peak decreased gradually and disappeared, and new peaks at 22.1 and 19.6 Å appeared when the percentages of Mg2+ and Ba2+ adsorbed increased on NaMnt. The peak shifted from 22.1 to 20.3 and 19.6 Å when the pH increased for all cations except Cd2+, which stayed constant at 22.1 Å. The coexistence of multiple d001 peaks in the XRD patterns suggested that the interlayer cations were segregated, and that the interlayer ion–ion interactions among different types of ions were minimized.