Focused ion beam nanotomography (FIB-nt) was applied to MX80 bentonite samples from the long-term Alternative Buffer Material (ABM) experiment in order to study the evolution of the intergranular pore space under similar condition that is supposed to prevail in repositories of nuclear waste. The applied high-resolution imaging method revealed the presence of two different types of pore filler. The first type is related to corrosion of iron and is represented by newly formed heavy minerals. Extensive formation of heavy minerals occurred only near the iron parts of the experimental set up. Based on comparison with other studies, the second filler type was interpreted as clay-gel that was likely formed during water uptake and swelling. A large fraction of the initial pore space was filled with such a clay gel. By attributing filled pores to the present open porosity, the initial intergranular porosity (radii > 10 nm) of the starting material was in the range of 4.3–4.6 vol.%, which was reduced to < 1 vol.% during the experiment. A finite scaling approach was applied to the initial pore space (i.e. pores with radii > 10 nm), which yielded percolation thresholds with critical porosities ϕ in the range of 3–19 vol.%. Thus, the residual open porosity was far below the percolation threshold.