1. We examined the effects of wind-induced mixing and particle resuspension on the pelagic food web in eutrophic shallow lakes. These processes are known to have a major impact on a variety of biological, physical or chemical parameters such as the underwater light climate, the nutrient availability in the water column and the abundance and composition of the phytoplankton community. However, little is known about the effects of these processes on other compartments of the freshwater food web.2. We conducted a 9-week experiment comprising a manipulation of mixing intensity in 15 m 3 mesocosms equipped with wavemakers in order to explore the impact of two mixing regimes on water chemistry as well as viral, bacterial, phytoplankton and zooplankton communities.3. The turbidity level in mixed mesocosms (compared to calm conditions) was higher on average, especially at the bottom, indicating a successful resuspension of the sediment bed. Mixing increased chlorophyll a concentration without any clear increase in algal abundance, measured as cell counts by flow cytometry, which pointed to a change in species composition or a physiological adaptation to mixing. pH increased strongly in mixed mesocosms, suggesting enhanced primary productivity in perturbed conditions. Zooplankton responses to mixing were neutral for cladocerans and negative for copepods, which potentially mediated top-down controls on the rotifer population.4. Bacterial and viral abundances were not significantly changed by the mixing regimes; however, peaks of viral lysis of heterotrophic bacteria were seen in each mixed mesocosm, while none were observed in calm mesocosms. These results suggest that viral lysis is enhanced by the water column mixing.5. Our experiment demonstrates that mixing is likely to influence shallow lake functioning through a complex combination of direct and indirect effects on the underwater light climate and water chemistry, phytoplankton physiology and productivity, zooplankton growth and possibly virus-host interactions. These complex effects could play a major role in structuring pelagic and benthic communities in shallow lakes