Biofilms, consisting of microorganisms in a matrix of organic and inorganic material, coat many particles in fluvial systems. These films play a dynamic role in the sorption and transport of hydrophobic contaminants. This project investigates the biosorption of pollutants in two agricultural headwaters of Germany. Here, biofilms contain, on average, three times the organic matter of river sediments, higher loadings of Cu, Fe, Mn and Zn but less Pb than the surrounding river sediments. The biofilms are most active in the sorption of heavy metals in the summer months but high variability reflects the occurrence both sorption and desorption processes. Organic pollutants such as PCB and PAH are concentrated in the summer and desorbed during the autumn months. In summer low water conditions, biosorption is an important factor in the accumulation of pollutants on river sediments. However, biofilms are liable to damage due to changes in nutrient supply and flood events. Sediment particles trapped during low flow condition are enriched in pollutants then resuspended during floods. Thus biofilms may act as either pollutant sinks or pollutant sources.