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 in-depth 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.