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In saturated bentonite, free water is hosted in the meso- and macropores. Microscopic characterization of free water and the associated pore structure is very difficult because of the swelling- and shrinking-behaviour of montmorillonite. In this article, we present state of the art cryo-preparation techniques including high pressure freezing and low temperature freeze substitution, which enable the stabilization of bentonite microstructures. Microscopic analyses of cryo-stabilized bentonite samples are then performed with conventional SEM, with cryo-SEM and with FIB-nanotomography. From the resulting 2D- and 3D- images, so-called “continuous pore size distributions” are calculated and the 3D-connectivities of the mesopores are documented. Furthermore, from the comparison with pore size analyses that are based on conventional preparation techniques (oven drying and freeze drying), it is shown that high pressure freezing leads to more reliable results. Overall, it is demonstrated that reliable quantitative 3D- characterization can be achieved from the bentonite pore structure when high resolution 3D-imaging by FIB- nanotomography is combined with modern cryo-preparation techniques (i.e. high pressure freezing).