The pollutant dynamics of estuaries is closely associated with the transport of paniculate matter and one problematic area is the quantification of the erosion, deposition and transport of intertidal sediment. The primary event in sediment erosion is the resuspension of surficial layers which are often densely colonized by assemblages of microphytobenthos and bacteria. The dominant microphytobenthos (Bacillariophyceae or diatoms) contain characteristic marker pigments, chlorophyll c_and fucoxanthin. To date, few marker compounds have been used to characterize paniculate matter and to monitor its transport. This study identifies pigments as useful marker compounds in monitoring erosive events, particularly at low erosion rates. Erosion can either be considered as occurring when the stress at the surface exceeds the threshold strength of the bed or as one side of a deposition/ entrainment equilibrium always occurring at the bed surface. The present analysis indicates that an erosion threshold exists and that pigments derived from surface biofilms appear in the water column before the general failure of the bed. The result is a lower yield stress (Uni) for biofilm components than for the sediments themselves, supporting the contention that the 'yield stress' of natural sediments has a strong biological component, in addition to purely physical control. Pigment fingerprinting is shown to provide information on the origin of suspended matter, including the suspension and deposition of particles. The potential for using microphytobenthic pigments as indicators of erosion events in laboratory simulations (erosion and respiration chambers) and in the field is discussed.