Studies of the subsurface microbiology of the Äspö Hard Rock Laboratory, Sweden have revealed the presence of many different bacteria in the deep groundwaters which appear to maintain reducing conditions. Experiments were conducted to study the rock-water and microbial interactions. These used crushed Äspö diorite, Äspö groundwater and iron- and sulphate-reducing bacteria in flowing systems under anaerobic conditions. In column experiments, there was evidence of loss and mobilization of fine-grained crushed material (<5 μm) which had originally adhered to grain surfaces in the starting material. The mobilized fines were trapped between grains. The degree of mineralogical alteration was greater in the experiments when bacteria were present. In both column and continuously stirred reactor experiments, there is evidence for the formation of a secondary clay. These experiments have shown that microbial activity can influence rock-water interactions even in nutrient-poor conditions.