This paper investigates the effects of the fungicide azoxystrobin, a compound widely used in rice farming, on aquatic communities representative of two habitats characteristic of Mediterranean wetland ecosystems: water springs and eutrophic lake waters. The long-term effects of azoxystrobin were evaluated on several structural (phytoplankton, zooplankton, macroinvertebrate populations and communities) and functional (microbial decomposition, macrophyte and periphyton growth) parameters making use of freshwater mesocosms. Azoxystrobin was applied in two pulses of 2, 20, 200 mu g/L separated by 14 d using the commercial product ORTIVA (23 % azoxystrobin w/w). The results show that these two habitats responded differently to the fungicide application due to their distinct physico-chemical, functional, and structural characteristics. Although overall sensitivity was found to be similar between the two (lowest NOEC < 2 mu g/L), the taxa and processes that were affected differed substantially. In general, the most sensitive species to the fungicide were found in the water spring mesocosms, with some species of phytoplankton (Nitzschia sp.) or macrocrustaceans (Echinogammarus sp. and Dugastella valentina) being significantly affected at 2 mu g/L. In the eutrophic lake mesocosms, effects were found on phytoplankton taxa (Desmodesmus sp. and Coelastrum sp.), on numerous zooplankton taxa, on chironomids and on the beetle Colymbetes fuscus, although at higher concentrations. The hemipteran Micronecta scholtzi was affected in both treatments. In addition, functional parameters such as organic matter decomposition or macrophyte growth were also affected at relatively low concentrations (NOEC 2 mu g/L). Structural Equation Modelling was used to shed light on the indirect effects caused by azoxystrobin on the ecosystem. These results show that azoxystrobin is likely to pose structural and functional effects on Mediterranean wetland ecosystems at environmentally relevant concentrations. Moreover, it highlights the need to consider habitat-specific features when conducting ecotoxicological research at the population and community levels.