In underground repository concepts for radioactive waste, bentonite is studied as a reference swelling material to be used as an engineered barrier. Under the changing geochemical conditions prevailing within the barrier (saturation with the fluid coming from the host formation, diffusion of various chemical plumes caused by the degradation of some constituents of the barrier-system, etc.), the surface chemistry of the clay particles could evolve. This work aims to characterize the effects of these changes on (i) the microstructure of compacted bentonite samples and (ii) the diffusion properties of HTO and Na in these samples. For this purpose, bentonite sets were equilibrated with different solutions: NaCl, CaCl2, CsCl solutions as well as an artificial clayey porewater solution. The microstructure of the different samples was characterized by HRTEM and XRD, in a water saturated state. In parallel, effective diffusion coefficients of both HTO and 22Na were measured for the different samples. The density of the bentonite in the diffusion tests and in the HRTEM observations was set at 1.6 Mg m−3. From the microstructural observations and the results of diffusion tests, it is deduced that one key parameter is the occurrence of a gel phase in the material, which is found to depend strongly on the bentonite set: the gel phase dominates in Na-bentonite, while it is lacking in Cs-bentonite. The HTO diffusion coefficients are found to be lower in the samples with high gel phase content. Sodium diffusion does not follow the same trend: when compared with HTO, Na diffuses faster when the gel phase content is high. The latter result could indicate that the “accelerated diffusion mechanism” of cations, already mentioned in the literature, is enhanced in clayey materials that contain a gel phase.