Microbial communities developing in biofilms have a major effect in lotic ecosystems, through the contribution of bacterial communities to biogeochemical cycles and through algae primary production. However, biofilms development is known to be dependent on environmental physical factors such as lighting, hydraulic turbulence or stream velocity (Guash and Sabater 1995, Biggs 2000). Most studies have enlightened the effect of major variations in these physical factors affecting strongly the community structure and diversity. Yet, most environmental changes are gradual, leading to subtle modifications in biofilm structure. In order to use biofilms as bio-indicators of natural aquatic environment, especially for environments undergoing chemical pressures, it is necessary to discriminate between the effects of chemicals and the effects of small physical changes. We used small indoors artificial streams to assess the effect on biofilm microbial communities of small modifications of three physical parameters: stream velocity, light intensity, presence of hydraulic turbulence. Microbial communities were studied throughout the experiment for their structure and their functioning. Stream velocity appeared to have the strongest and earliest effect on communities, while light intensity took effect lately. No effect of hydraulic turbulences was detected at the level used in the experiment. Impacts on communities were observed mostly on organic dry matter, cellular abundance and production, when diversity modifications were reduced. Subtle changes in physical factors were experimentally shown to affect biofilm structure and functioning, and have to be taken properly into account in upcoming field studies intending to assess the use of biofilms for bio-indication.