Landfill and radioactive waste disposal risk assessments focus on contaminant transport and are principally concerned with understanding the movement of gas, water and solutes through engineered barriers and natural groundwater systems. However, microbiological activity can affect transport processes, changing the chemical and physical characteristics of the subsurface environment. Such effects are generally caused by biofilms attached to rock surfaces. Currently most existing transport models have to introduce additional assumptions about the relationships between the microbial growth and changes to the porosity and permeability. These relationships are particularly poorly understood. This paper reviews recent experimental work directed at the development of biofilms and their influence on subsurface flow and the transport of contaminants in intergranular and fracture porosity flow systems. The results are then discussed in terms of a more complex conceptual model.