Among the most important stressors for aquatic ecosystems in the future are global warming and ocean acidification. To investigate their direct and indirect effects on a near-natural plankton community, a large-scale approach is needed. Therefore, four mesocosm experiments were conducted within the BIOACID II framework, using plankton communities from the Baltic Sea, North Sea and Atlantic Ocean. The focus of this project was on the pivotal role of microzooplankton (MZP) as trophic intermediary between the microbial loop and higher trophic levels. At the base of the food web, MZP has a strong impact on phytoplankton standing stocks due to high growth and grazing rates, leading to dietary competition with mesozooplankton. Thus, data on MZP abundance, biomass and taxonomic composition was analysed with emphasis on phytoplankton-MZP-mesozooplankton interactions. In conclusion, warming can be expected to directly affect MZP communities and enhance their growth and grazing pressure. In contrast, the results point at more complex responses of MZP to an increase in pCO2. While direct effects on the MZP community could not be observed, the present data points at predominately indirect effects via e.g. changes in phytoplankton community composition and/or standing stocks. Such indirect alterations might, however, be compensated on an ecosystem level.