We report some recent applications of multiscale modelling to the transport of ions, water and CO₂ in clays. On the one hand, simulations on different scales allow us to investigate the physicochemical processes underlying the geochemical and transport behaviour of these fluids in the interparticle pores and at the surface of clay minerals. We discuss more specifically the insights gained from molecular simulations into the acidity of surface edge sites, ion exchange and the behaviour of clay interlayers in contact with a CO₂ reservoir. On the other hand, upscaling the descriptions from the molecular level to the macroscopic scale without forgetting the fundamental role of interfaces on the mesoscopic scale provides a means to capture complex phenomena such as electrokinetic couplings. We illustrate the complementarity of molecular dynamics, lattice-based mesoscopic simulations and Pore Network Models to address this issue.