Clay minerals are used in a wide number of natural or artificial materials for municipal or nuclear waste management in which water diffusion is the principal transfer process. However, a quantitative assessment of the impact of the preferred orientation of lamellar clay particles on water diffusion is still lacking. Using 3D Brownian dynamics simulation on representative virtual clay porous media, a systematic study of water diffusion for single-porosity (illite or kaolinite) and dual-porosity (vermiculite) systems was conducted. The simulated water diffusion coefficients were validated through comparison with experiments and were used to build an Archie model including the degree of anisotropy in particle orientation. The results showed that water diffusion can be predicted based on a correct description of the solid phase organization and that clay particle orientation, such as interparticle porosity, is a primary parameter governing water mobility. Moreover, the anisotropy of water diffusion can be linked to the degree of particle preferred orientation, irrespective of the porosity value. The modified version of the Archie model for water diffusion in clay systems proposed here has many potential applications where decoupling of porosity and preferred orientation is needed, including better prediction of water transfers or improved designs of clay liners with sustainable use of natural mineral resources.