This study investigates the influence of microbes on fluid transport in sedimentary and igneous host rock environments. It particularly focuses on granodiorite rock (Äspö; Sweden) and mudstone (Horonobe; Japan) that were utilised during laboratory-based column experiments. The results showed that biofilms form on both rock types in low nutrient conditions. Cryogenic scanning electron microscopy showed that the morphology of biofilaments varied from filamentous meshwork (in crushed granodiorite column experiments) to clusters of rod-like cells (fracture surfaces in mudstone). X-ray diffraction analysis of the fine fractions (<5 µm) revealed the formation of secondary clay mineral phases within the crushed Äspö granodiorite rock substrate only. The formation of secondary clay minerals appears to be enhanced when bacteria are present. All experiments showed biofilm formation, bacterial enhanced trapping of fines blocking off pore throats and/or secondary clay mineral formation. These observations illustrate the importance of bacteria on rock transport properties which will impact on the containment and migration of contaminants.