Abstract Long term integrated in situ experiments are performed in the HADES underground research facility (Mol, Belgium) in order to study the coupled reactivity between the different components of an underground repository for vitrified high level radioactive waste (HLW): glass, compacted clay, and stainless steel containers, at 90 °C and under gamma irradiation. Studies pertaining to the behaviour of silicon, a major element released during glass alteration, are presented here. Data collected from the integrated experiment, from simplified tests, and from modelling are put together, giving complementary information. The integrated experiment is used to investigate overall reactivity, whereas diffusion experiments coupled with modelling focused on the precipitation of silica in clay media. In the integrated in situ experiment, a bentonite clay (FoCa7) mixed with 5 wt.% of powdered glass frit was put in contact with U/Th-doped SON68 reference glass specimens for 1.2 years. One of the samples was thoroughly analysed by ESEM, SEM-EDS, TEM, XRD, and FTIR. The observations showed that after combined heating and γ irradiation, the glass/clay interface is still fully reactive. At this interface, the most important process occurring is silica precipitation either as spherical flaky nodules, or in the form of coatings on the clay surface, as chalcedony and amorphous silica. In parallel, numerical modelling was used to investigate the interactions between silica and clay material in a simplified experiment using diffusion cells. A fit between calculation results and silica migration measurements in diffusion cells was performed, including sensitivity tests with regard to the diffusion coefficients and the precipitation rate of amorphous silica. A satisfactory agreement is reached with the experimental results, using a set of reasonable fitting parameters for the FoCa7 clay material. Surface area values for silica precipitation are found to be very high, i.e. 2% of the total surface area of the clayey material indicating that silica precipitation occurs on surfaces other than those of pure silica minerals.