Bentonite clay is planned to form a part of deep-geological repositories of spent nuclear fuel in several countries. The extremely long operation time of the repository requires an indepth understanding of the structure and properties of used materials. In this work the microstructure of a simplified system of Ca-montmorillonite is investigated using a set of complementary methods: X-ray diffraction, small angle X-ray scattering, nuclear magnetic resonance, transmission electron microscopy and ion exclusion. The paper presents experimental results obtained from compacted, water saturated samples in the dry density range 0.6–1.5 g/cm3. It can be observed that different methods yield similar quantification of water present in the interlamellar space. Combined results support the multiple porosity concept of the bentonite structure.