This data set contains supporting data for figures in the main text of the publication and the supporting information. Our data will be of major interest to a broad audience, as they represent experimental data derived from a diversity manipulated complex natural plankton community, thereby reflecting a realistic natural scenario. With this study we were able to show how a biodiversity loss in plankton communities can influence the phytoplankton – zooplankton interface in terms of providing important food quality traits by the phytoplankton influencing the zooplankton community. The significance of the multi-year large-scale mesocosm study data presented here is to support important mechanistic findings from former mainly laboratory studies showing the importance of essential fatty acids in dependence of biodiversity in natural phytoplankton communities.