Biofilms in surface waters primarily consist of allochthonous microorganisms. Under conditions of pollution faecally derived bacteria may interact with these biofilms. Total coliform bacteria, Escherichia coli and intestinal enterococci are used to monitor source water quality, indicating faecal pollution and the possible presence of enteric pathogens. In the present study the occurrence of faecal indicators was investigated in biofilms (epilithic biofilms, sediments) of German rivers. All of the biofilms contained significant concentrations of these bacteria, which were several orders of magnitude lower compared with the total cell number and the number of culturable heterotrophic plate count bacteria indicating that faecal indicator bacteria represented a minor fraction of the whole biofilm communities. The biofilms displayed approximately two orders of magnitude higher concentrations of total coliforms, E. coli and enterococci compared with the overlying water. Identification of coliform and enterococcal isolates from the biofilms revealed the presence of species which are known to be opportunistic pathogens. Overall, the results of the present study show that faecal indicator bacteria can survive in the presence of high cell densities of the authochthonous microflora in epilithic biofilms and sediments, suggesting that these biofilms may act as a reservoir for bacterial pathogens in polluted rivers.