This study is the first attempt to generate a realistic model for the clay–cation–water system. We use a molecular description of the solvent and clay sheet. We have chosen two clay materials from 2:1 dioctahedral smectites (1) montmorillonite and (2) beidellite to monitor the effect of negative charge on the location of interlayer cation (Na +), as the negative charge gets introduced in the clay system from octahedral Al substitution and tetrahedral Si substitution as the case may be (1) and (2), respectively. We use Grand Canonical Monte Carlo (GCMC) simulation to locate the interlayer cation and to calculate the number of interlayer water molecules surrounding the cation (Na +) for both the clay materials. The results show that each Na + cation is surrounded by five water molecules. The minimum energy conformer obtained from GCMC calculations has been used to generate the cluster model for Local Density Functional (LDF) calculations. The results show the Na + cation moves towards the negative center of the clay cluster. It is also observed that Na + cation gets more stabilized in montmorillonite in comparison to beidellite.