Abstract Hydrogen gas was injected, together with helium and neon, into a borehole in the low-diffusivity Opalinus Clay rock. The hydrogen partial pressure was at most 60 mbar. A water production flow rate from the surrounding rock of c. 15 ml/day had been obtained previously, indicating that the test interval wall was presumably saturated with water. Helium and neon concentrations decreased as expected while taking into account dissolution and diffusion processes in the porewater. In contrast, the disappearance rate of hydrogen observed (2×10 −4 to 3×10 −4 mol/day/m 2 ) was c. 20 times larger than the calculated rate considering only dissolution and diffusion. The same rate was observed following a new hydrogen injection and over a six-month semi-continuous injection phase. Simultaneously, sulphate and iron concentrations decreased in the water, whereas sulphide became detectable. These evolutions may be due to biotic processes involving hydrogen oxidation, sulphate reduction and Fe(III) reduction.