Hydrogen (H2) was injected into a shallow aquifer at the TestUM field site (close to Wittstock, Brandenburg, Germany) in order to simulate a H2 gas leakage scenario. The resulting biogeochemical processes were monitored in space and time by analyses of stables hydrogen isotopes, groundwater microbial community composition and geochemical parameters in two monitoring wells (D04, D06) close to the injection wells, and a reference well (D11) not directly affected by the injected H2. During the injection, initial shifts in the isotope signature of H2 were observed, probably caused by dissolution of H2 in the water phase and the migration of the gas phase through pores and channels in the aquifer. After the injection, H2 concentrations in D04 and D06 decreased within less than 80 days from maximal 850 µmol/L below the detection limit, accompanied by an equilibrium isotope exchange with water leading to a strong isotopic depletion of H2, a reaction typically catalyzed by the H2-cleaving enzyme hydrogenase. Microbial H2 oxidation and subsequent growth of hydrogenotrophic prokaryotes was further indicated by temporally increasing abundances of putative H2-oxidizing sulfate reducers, acetogens, nitrate reducers and aerobes, accompanied by nitrate disappearance and transiently increasing acetate concentrations. In summary, the results confirm our expectation that H2, being an excellent energy source for many microorganisms, is quickly microbiologically consumed in an aquifer after a leakage.