Microbial activity can have a significant impact on geochemical processes as it can influence mineral dissolution and precipitation, pH, alkalinity and redox. Experiments were conducted to study the rock-water and microbial interactions, specifically to examine the influence of microbes on the groundwater environment in fractured crystalline rock. These used combinations of crushed Äspö Diorite, Äspö groundwater with iron and sulphate reducing bacteria in columns and continuously stirred tank reactors under both anaerobic and aerobic conditions. Results showed loss (dissolution and/or mobilization) of fine grained crushed material (<50 μm) which had originally adhered to grain surfaces in the starting material. The mobilized fines were subsequently trapped on biofilms developed between grains. There was also evidence for the formation of smectite (not present in the starting materials) which, together with the trapping of translocated fines in intergranular pore throats by biofilms, resulted in blockage of the column experiments. The degree of mineralogical alteration and/or pore blocking was greater in the experiments when bacteria were present and occurred under anaerobic conditions. Little evidence for rock-water interactions was seen in the chemical analysis data for all the experiments. Modelling of the fluids showed them to be saturated with respect to clay minerals. The observed mineralogical changes seem to reflect alteration occurring in microbially mediated microenvironments close to mineral surfaces. Consequently, these changes may be too small to be detected by the chemical analysis of the bulk fluid. These experiments have shown that microbial activity can impact on fluid flow through porous media even in nutrient poor conditions. In addition, the formation of new clay minerals on pore-surfaces is potentially important for ion exchange and sorption reactions.