The in situ porewater chemistry (PC) experiment carried out in the Opalinus Clay formation at the Mont Terri Rock Laboratory, Switzerland for a period of 5 a allowed the identification and quantification of the biogeochemical processes resulting from and affected by an anaerobic microbial disturbance. The unintentional release of degradable organic compounds (mainly glycerol) induced microbially-mediated SO4 reduction in the borehole with concomitant significant geochemical changes in the circulating water and the adjacent porewater. These changes included a decrease in SO4 concentration and pH and an increase in pCO2 and alkalinity relative to the non-affected formation water. However, the cation composition of the water and the mineralogy of the clay close to the borehole wall showed very little change. This is explained by (1) the strong chemical buffering processes in the clay and (2) by the diffusion-limited flux of solutes. With the aid of a reactive transport model with a minimum set of kinetic parameters for the hypothesised degradation reactions, the evolution of solutes in the borehole could be modelled adequately. The model was also applied to the prediction of restoration times upon depletion of the C source and results indicated restoration times to undisturbed conditions of about 15 a, but also highlighted the rather large uncertainties inherent in the geochemical model. Nevertheless, the simulations provided additional evidence of the high pH buffer capacity of the Opalinus Clay. The results from the microbiological investigations do not allow unambiguous identification of the origin of the microbial population in the borehole. Possible sources were the drilling procedure, the artificial porewater, and perhaps some revival of indigenous dormant strains. Regardless of the origin of the microbes, the results from the PC experiment underlined the importance of anaerobic microbial activity in the ''disturbed'' Opalinus Clay, facilitated by the introduction of space, water and organic material, in rapidly establishing very reducing conditions. The PC experiment also yielded valuable insight with regard to the safety of a high-level radioactive waste repository emplaced in Opalinus Clay. Anaerobic microbial perturbations in the clay host rock may occur from the construction and excavation procedures and emplaced organic by-products. The resulting effects on porewater chemistry, i.e., especially on pH and Eh, may affect the mobility of radionuclides eventually released from the waste. However, the overall results of the PC experiment suggest that such effects are temporary and spatially limited because of the large buffering capacity and diffusive properties of the clay formation. Nevertheless, the results also indicate that the amounts of organic materials in a high-level waste repository should be kept small in order to achieve background conditions within a short time period after repository closure. A further conclusion from the PC experiment is that commonly used equipment materials may not display commonly assumed inert behaviour. This particularly holds for the gel-type ''robust'' reference electrodes, which may release substantial amounts of glycerol.