The ecological role of toxin production in cyanobacteria is still unknown. Here, we studied the potential effect of different zooplankton taxa and density on growth and toxin production of the cyanobacterium Nodularia spumigena. In this experiment, N. spumigena was exposed to three different zooplankton taxa: Rotifera (Synchaeta baltica), Copepoda (Eurytemora affinis) and Cladocera (Daphnia magna) and as a comparison a zooplankton free control. We used false bottom chambers separating the cyanobacterium and zooplankton and were thereby able to prevent direct grazing. Overall, N. spumigena toxin levels (nodularin expressed as microcystin equivalents) were significantly lower when exposed to the different zooplankton compared to the zooplankton free control, whereas no effects could be detected on N. spumigena growth and biomass. Although we did not test the underlying mechanism, these findings suggest that the presence of zooplankton reduce toxin production in N. spumigena, independent of growth. Therefore, toxin production in N. spumigena should not be considered an induced defence mechanism against zooplankton, at least not on a short‐term basis.