Aquatic ecosystems face a multitude of environmental stressors, including warming and acidification. While warming is expected to have a pronounced effect on plankton communities, many components of the plankton seem fairly robust towards realistic end-of-century acidification conditions. However, interactions of the two stressors and the inclusion of further factors such as nutrient concentration and trophic interactions are expected to change this outcome. We investigated the effects of warming and high CO2 on a nutrient-deplete late summer plankton community from the Kiel Fjord, Baltic Sea, using a mesocosm setup crossing two temperatures with a gradient of CO2. Phytoplankton and microzooplankton (MZP) growth rates as well as biomass, taxonomic composition, and grazing rates of MZP were analysed. We observed effects of high CO2, warming, and their interactions on all measured parameters. The occurrence and direction of the effects were dependent on the phytoplankton or MZP community composition. In addition, the abundance of small-sized phytoplankton was identified as one of the most important factors in shaping the MZP community composition. Overall, our results indicate that an estuarine MZP community used to strong natural fluctuations in CO2 can still be affected by a moderate increase in CO2 if it occurs in combination with warming and during a nutrient-deplete post-bloom situation. This highlights the importance of including trophic interactions and seasonality aspects when assessing climate change effects on marine zooplankton communities.