This paper evaluates the effects of different time-varying exposure patterns of the strobilurin fungicide azoxystrobin on freshwater microsocosm communities. These exposure patterns included two treatments with a similar peak but different time-weighted average (TWA) concentrations, and two treatments with similar TWA but different peak concentrations. The experiment was carried out in outdoor microcosms under four different exposure regimes; (1) a continuous application treatment of 10 μg/L (CAT(10)) for 42 days (2), a continuous application treatment of 33 μg/L (CAT(33)) for 42 days (3), a single application treatment of 33 μg/L (SAT(33)) and (4) a four application treatment of 16 μg/L (FAT(16)), with a time interval of 10 days. Mean measured 42-d TWA concentrations in the different treatments were 9.4 μg/L (CAT(10)), 32.8 μg/L (CAT(33)), 14.9 μg/L (SAT(33)) and 14.7 μg/L (FAT(16)). Multivariate analyses demonstrated significant changes in zooplankton community structure in all but the CAT(10) treated microcosms relative to that of controls. The largest adverse effects were reported for zooplankton taxa belonging to Copepoda and Cladocera. By the end of the experimental period (day 42 after treatment), community effects were of similar magnitude for the pulsed treatment regimes, although the magnitude of the initial effect was larger in the SAT(33) treatment. This indicates that for long-term effects the TWA is more important for most zooplankton species in the test system than the peak concentration. Azoxystrobin only slightly affected some species of the macroinvertebrate, phytoplankton and macrophyte assemblages. The overall no observed ecologically adverse effect concentrations (NOEAEC) in this study was 10 µg/L.