The two-dimensional interlayer space of layered materials has been highlighted due to their adsorption property, whose nanostructure in the water-immersed state is scarcely understood by experiment. Recent developments in molecular simulation have enabled researchers to investigate the interlayer structure, but water content is necessary for accurate modeling. In the present study, we proposed a theoretical method to estimate the saturated water content and adsorption selectivity of trichlorophenol and phenol in montmorillonite modified with hexadecyltrimethylammonium ions. By analyzing non-bond energy in interlayer water and following comparison with the bulk water model, the saturated water content was estimated to be between 12.7 and 14.2 wt %, which is consistent with the corresponding thermogravimetry data. In the water-immersed state, trichlorophenol was distributed in the center of the interlayer due to the van der Waals interaction with the organocation. Solvation free energy analysis revealed that trichlorophenol was more stable in the interlayer than in the aqueous solution, while the opposite result was obtained for phenol, reproducing the adsorption selectivity reported experimentally. Thus, it was found that both the saturated water content and adsorption selectivity are predicted by molecular simulation. The adsorption site of trichlorophenol changed from the center of the interlayer to the clay surface in the dry state, indicating that accurate modeling in the water-immersed state is significant for revealing the adsorption structure.