Abstract. Community approaches to investigating ocean acidification (OA) effects suggest a high tolerance of micro- and mesozooplankton to carbonate chemistry changes expected to occur within this century. Plankton communities in the coastal areas of the Baltic Sea frequently experience pH variations partly exceeding projections for the near future both on a diurnal and seasonal basis. We conducted a large-scale mesocosm CO₂ enrichment experiment ( ∼  55 m³) enclosing the natural plankton community in Tvärminne–Storfjärden for 8 weeks during June–August 2012 and studied community and species–taxon response of ciliates and mesozooplankton to CO₂ elevations expected for this century. In addition to the response to fCO₂, we also considered temperature and chlorophyll a variations in our analyses. Shannon diversity of ciliates significantly decreased with fCO₂ and temperature with a greater dominance of smaller species. The mixotrophic Myrionecta rubra seemed to indirectly and directly benefit from higher CO₂ concentrations in the post-bloom phase through increased occurrence of picoeukaryotes (most likely Cryptophytes) and Dinophyta at higher CO₂ levels. With respect to mesozooplankton, we did not detect significant effects for either total abundance or for Shannon diversity. The cladocera Bosmina sp. occurred at distinctly higher abundance for a short time period during the second half of the experiment in three of the CO₂-enriched mesocosms except for the highest CO₂ level. The ratio of Bosmina sp. with empty to embryo- or resting-egg-bearing brood chambers, however, was significantly affected by CO₂, temperature, and chlorophyll a. An indirect CO₂ effect via increased food availability (Cyanobacteria) stimulating Bosmina sp. reproduction cannot be ruled out. Although increased regenerated primary production diminishes trophic transfer in general, the presence of organisms able to graze on bacteria such as cladocerans may positively impact organic matter transfer to higher trophic levels. Thus, under increasing OA in cladoceran-dominated mesozooplankton communities, the importance of the microbial loop in the pelagic zone may be temporarily enhanced and carbon transfer to higher trophic levels may be stimulated.