Small streams are ecosystems mainly controlled by physical factors. Minor differences in these factors can affect periphyton, which are key functional communities in these ecosystems. Eight different environmental conditions combining two types of current, two flow velocities and two light intensities were produced and controlled in artificial channels. Their impact on young and mature periphyton was investigated during a 6-week exposure period. The two different levels of light intensity produced early effects on the algal community. In young periphyton, the lower level of light intensity enhanced the number of algal cells, and this community appeared to be significantly structured by light. As the periphyton matured, the effects of physical factors became more marked. At this later stage, both the bacterial and algal communities began to be affected. Both function (primary production) and structure began to respond to differences in light and in flow velocity. Small differences in low-level environmental factors, such as light and flow, had an effect both on the structure of periphyton and its functional capacities. Keeping in mind the close link between diversity and function in microbial communities, periphyton confronted to various environmental stresses (pollution, flooding) in the field may behave differently due to minor differences in physical factors.