Lake and river environments in wine-producing watersheds receive large inputs of phytosanitary products (herbicides, fungicides, insecticides) mainly arriving through runoff during rainfall events. The present study evaluates the sensitivity of aquatic microbial communities from stream (la Morcille, E France) and lake (Léman and Aiguebelette, E France) environments to the organic fungicide Tebuconazole (TBZ). The TBZ is an inhibitor of the ergosterol biosynthesis and is expected to mainly affect fungi, but algae and bacteria may also be impacted by direct and/or indirect effects. Biofilm and plankton communities from reference and polluted sites in the two type of aquatic environments were exposed to low (2 mg/L) and high (20 mg/L) nominal concentrations of TBZ plus control conditions in microcosms experiments. The response of microbial communities was evaluated at the structural level (abundance, diversity) and functional level (primary production, respiration). Pesticide concentrations were also monitored throughout the experiments. Results showed that biofilms were highly reactive and had strong TBZ-degrading capacities (60-70% degradation after 3-weeks), whereas impact on plankton communities was negligible. In stream biofilms, TBZ decreased photosynthetic efficiency and heterotrophic respiration especially at the reference site. Instead, changes in algal and bacterial abundances were transient, but the proportion of dead bacterial cells increased. Responses of planktonic communities were rather different than on biofilms, bacterial abundances and esterase activity being favored by TBZ exposure. The present microcosm experiments evidenced that the functioning of microbial communities in aquatic environments can be significantly impacted by chronic TBZ exposure. The different sensitivity between biofilms and plankton communities might be explained by the different community structure and absorption modes of the pesticide. Further analyses on bacterial diversity could give some light on the tolerant species to this fungicide.