ABSTRACT.    Natural ecosystems are widely influenced by human activities, especially agricultural practices that include the extensive uses of xenobiotics such as herbicides. By soil leaching and overland flow, most of these organic molecules leads to surface water contamination (lakes and rivers), where they can affect the autotrophic communities of the natural ecosystems. The release of organic coumpounds from the altered algal communities can indirectly disturb the heterotrophic bacterial community that play a key role in aquatic environments, and consecutively all the living microorganisms involved in the trophic chain. Therefore the modifications induced by the presence of organic compounds could provide selective pressure that promote the emergence of water-borne pathogens, either microorganisms naturally able to growth in water or coming from fecal sources. Most of the bacteria in water are associated with biofilms on liquid - solid surfaces. They represent environments with special features that render them most exposed to xenobiotics. Natural biofilms were grown on glass substratum and incubated into a river linked to river bed monitored by a pesticide pollution watch net. The bacterial density (1.7- 3.5cell/cm²) is comparable to those reported in literature. The percentage of CTC-positive cells is twice more important. The analysis of the bacterial community structure by FISH reveals the dominance of bacteria related to CFB group. The presence of specific procaryotic pathogens, i.e. Enterobacteria, was detected by specific PCR using the genomic DNA from the total biomass as template. In parallel, aliquots of the bacterial suspensions were plated on Enterobacteriaceae selective media and the isolates were phenotypically identified and their antibiotic resistance pattern were demonstrated (beta-lactamase). We will propose now to determine the influence of three different herbicides (diuron, glyphosphate and AMPA) on the development of periphytic microbial communities within biofilms.