Clay-rich media have been proposed as engineered barrier materials or host rocks for high level radioactive waste repositories in several countries. Hence, a detailed understanding of adsorption and diffusion in these materials is needed, not only for radioactive contaminants, but also for predominant earth metals, which can affect radionuclide speciation and diffusion. The prediction of adsorption and diffusion in clay-rich media, however, is complicated by the similarity between the width of clay nanopores and the thickness of the electrical double layer (EDL) at charged clay mineral–water interfaces. Because of this similarity, the distinction between ‘bulk liquid’ water and ‘surface’ water (i.e., EDL water) in clayey media can be ambiguous. Hence, the goal of this study was to examine the ability of existing pore scale conceptual models (single porosity models) to link molecular and macroscopic scale data on adsorption and diffusion in compacted smectite. Macroscopic scale measurements of the adsorption and diffusion of calcium, bromide, and tritiated water in Na-montmorillonite were modeled using a multi-component reactive transport approach while testing a variety of conceptual models of pore scale properties (adsorption and diffusion in individual pores). Molecular dynamics (MD) simulations were carried out under conditions similar to those of our macroscopic scale diffusion experiments to help constrain the pore scale models. Our results indicate that single porosity models cannot be simultaneously consistent with our MD simulation results and our macroscopic scale diffusion data. A dual porosity model, which allows for the existence of a significant fraction of bulk liquid water—even at conditions where the average pore width is only a few nanometers—may be required to describe both pore scale and macroscopic scale data.