To contain domestic waste and its associated pollution within a landfill, engineered mineral (clay) barriers are used and are designed to have a permeability of 1 x 10(-9) m/s (Westlake 1995). The rate of permeability of various porous media has shown to be influenced by the clogging of flow paths (media pores) due to biofilm formation (Charckalis and Marshall 1990, Cunningham et al. 1991). The term biofilm is given to describe the colonies of surface adherent microorganisms (Donlan et al. 1994). In this study, permeability experiments were built and modified to act as microcosms to investigate the influence of biofilm formation on the permeability of clay barriers. Traditional scanning electron microscopy methods disrupt or destroy the biofilm and previous anaerobic studies have involved building closed cells (such as miniature continuous culture chambers) that utilise light microscopes (Robin Jones et al. 1997). This paper examines the application of the environmental scanning electron microscope (ESEM) to the direct examination of the clay interface and biofilm formation in situ within the microcosm.