Layered minerals containing inter-layer water show directional anisotropy. In previous work, the authors have shown that this inter-layer water affects the mechanical performance of these minerals. Even though difference in thermal conductivity of minerals has been alluded to in experimental literature due to presence of water molecules within crystal, a detailed coordinated theoretical study has not been carried out. In this work, a molecular dynamics study has been presented on sulfates of calcium to demonstrate that thermal conductivity is indeed reduced with the presence of inter-layer water. The correlation between the vibration of different molecular groups to the thermal transport mechanism of the material has been investigated. It has been observed that vibration modes of H2O molecules have a negligible contribution to thermal transport eventually reducing thermal conductivity perpendicular to the water layer. Even though calcium sulfate has been chosen for this study, it can be anticipated that similar behaviors can be observed with other minerals in which inter-layer water is present. This study represents a detailed structure–property correlation in the thermal transport mechanism through layered minerals.