The planned final disposal repositories of spent nuclear fuel in several countries, including Finland, pose significant scientific challenges due to their extremely long lifespan. One of the key materials proposed for use in Posiva Oy's repository in Finland is MX-80 bentonite in a compacted, water-saturated state. Border cases of calcium and sodium forms of purified bentonite were included in this study. The MX-80 in the repository is expected to undergo cation exchange due to the composition of the groundwater. The clays were studied at different dry densities between 0.7 and 1.6 g cm–3. The microstructure of the water-saturated, compacted clays was investigated using small-angle X-ray scattering, nuclear magnetic resonance and transmission electron microscopy. Additionally, atomic force microscopy was used to characterize the shape and size of the fine-fraction clay platelets. As expected, the average shape of the fine fractions was smaller than the bulk material, but a more elongated shape was present in the purified material. Mainly due to sample density, the pore structure was noticeably different for the Na form of purified bentonite at 0.7 g cm–3 density, but at higher degrees of compaction, no significant differences were noted between the samples. The laboratory results obtained in this study could be useful for safety and performance analysis of this high-level waste repository where sodium bentonite is used and is expected to change its charge-compensating cation composition during the repository's lifetime. Microstructural data may be used in modelling of diffusion and sorption by surface complexation modelling, for example, or as a basis for mechanical and water transport models.