A series of batch laboratory experiments (‘black boxes’) were set up to study the gross effects of microbial activity on repository geochemistry, radionuclide sorption and the integrity of repository and host rock materials in a Swiss type B repository. The observed principal chemical exchanges and precipitations were confirmed by modelling and could be interpreted by excluding microbiological effects. However, mineralogical studies showed steel corrosion to be localised in deep pits with microbiology playing a possible role. Talc was precipitated in all of the cells which lowered ambient pH through removal of OH- causing dissolution of CSH compounds. This has implications for the long term stability of cements. Microbiology influenced far-field radiochemistry experiments in which added microbes increased Cs sorption particularly under anaerobic conditions.