1. The development of periphytic algae and bacteria is controlled by a combination of interacting biotic processes and abiotic factors. Distinguishing between the selection pressure resulting from pollution, and that of natural environmental factors is therefore one of the most critical aspects of assessing the impact of pollutants on the diversity and function of benthic microbial communities in natural ecosystems. 2. We studied how current velocity and season affect the ability of river biofilms to cope with complex chemical pollution. We compared the diversity, structure and production of periphytic algae and bacteria from four sampling zones with differing chemical water quality levels and different flow velocities over the course of two seasons (summer and winter). 3. The three factors tested all influenced biofilm development, but this depended on the biological variable being measured. Bacterial and algal densities were highly dependent on season and chemical water quality. Algal density was lower in summer than in winter, but bacterial density and production increased from upstream (reference) to downstream (polluted), and this increase was more marked in winter. The impact of chemical water quality was also dependent on the season. 4. An interaction between current velocity and pollution was also detected. During the summer, there was no difference in bacterial density or production between the upstream and downstream segments in the fast current zones, whereas both variables were higher downstream in the slow current zones. Such interactions between environmental factors and the impact of water quality on biofilms must be taken into account in assessments of the effects of chemicals on biofilm community structure and functioning in rivers.