The fluid dynamic gauging (FDG) technique was originally developed to monitor the thickness of soft fouling layers immersed in liquid to provide quantitative information on fouling and cleaning processes. The latest version of the technique, scanning zero net flow FDG, allows measurements to be made aseptically at different locations on the same sample. Its potential for studying the removal of high-risk soils is demonstrated in (i) quantifying the shear stress required to remove bacterial spores from glass and stainless steel, and (ii) measuring the rate of erosion of Rhodopseudomonas palustris biofilms from standard and graphene-coated carbon paper. The adhesion of Bacillus cereus and B. megaterium spores was shown to differ significantly between spore type, spore cultivation conditions and substrate. The characteristic shear stresses required to remove 50% of the spore lawns were significantly greater than those imposed by standard industrial pipe flows. The R. palustris biofilms were uneven, with thicknesses ranging from 120±37 to 280±98μm. The manner and rate of biofilm erosion was again strongly dependent on substrate. A new erosion modelling approach is presented which quantifies the differences in the biofilms in terms of erosion rate and strength. Biofilms grown on graphene were thinner, eroded more quickly and exhibited low adhesion strength.