The Hydrogen Transfer (HT) experiment, located at the Mont Terri underground rock laboratory in Switzerland, is an in situ experimental study of the interactions and transport of hydrogen injected into a borehole installed within Opalinus Clay, a claystone formation. A python-based model was developed to analyse and model the experimental data, for diffusion of dissolved gases and solutes in claystone pore water, for thermodynamic modelling of gas-water-solid phase equilibria in the injection interval and for simulations of chemical equilibria and reaction kinetics in claystone and injection interval. The developed model reproduces the temporal evolution of gas pressure, composition and solute concentrations measured in situ with a minimum set of adjustable parameters. The effective diffusion coefficients for dissolved gases in Opalinus Clay derived by the modelling of experimental data were found to be very close to values measured in other experimental studies. It was discovered that an accurate description of the temporal variations in hydrogen injection and temporal changes in the inflow of formation water is essential for modelling of microbial mediated hydrogen consumption in the injection interval.