Streams are often subjected to diffuse pollution, especially in extensive vineyard areas where the use of plaguicides is frequent. The main objective of this study was to determine the effects of TBZ (fungicide) in the structure and metabolism of algal and bacterial communities forming biofilms. Biofilms colonized in reference (Saint Joseph, SJO) and polluted (Saint Ennemond, SEN) stream sites from la Morcille stream (Beaujolais region, Eastern France) were exposed to two different TBZ dosages (2 mgTBZ/L; 20 mgTBZ/L plus controls). Biofilm structural (algal and bacterial abundances and community composition) and functional descriptors (primary production, respiration, metabolic diversity) were surveyed during a 22-days experiment by using artificial stream channels. We observed a decrease in the proportion of live/dead bacteria in biofilms from the two study sites (SJO and SEN). However, decreases in bacterial respiration and photosynthetic efficiency were only consistent in biofilms from the reference site (SJO), but not in those from the polluted site (SEN). The Biolog EcoPlates analysis determined that moderate dosages of TBZ (2mg/L) may homogenize the metabolic diversity between reference and polluted communities. TBZ inputs in streams may have consequences in ecosystem processes, such as the organic matter decomposition, since it decreases bacterial activity. But also, TBZ decreases the photosynthetic efficiency, and therefore, the potential primary production in the stream environment. Our results confirm that the TBZ (fungicide) has indirect effects on algal and bacterial communities, especially in those communities that has not been previously exposed to this toxicant.