About a quarter of anthropogenic CO.sub.2 emissions are currently taken up by the oceans, decreasing seawater pH. We performed a mesocosm experiment in the Baltic Sea in order to investigate the consequences of increasing CO.sub.2 levels on pelagic carbon fluxes. A gradient of different CO.sub.2 scenarios, ranging from ambient (ââ¼ââ¯370â¯Âµatm) to high (ââ¼ââ¯1200â¯Âµatm), were set up in mesocosm bags (ââ¼ââ¯55â¯m.sup.3). We determined standing stocks and temporal changes of total particulate carbon (TPC), dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), and particulate organic carbon (POC) of specific plankton groups. We also measured carbon flux via CO.sub.2 exchange with the atmosphere and sedimentation (export), and biological rate measurements of primary production, bacterial production, and total respiration. The experiment lasted for 44Â days and was divided into three different phases (I: t0-t16; II: t17-t30; III: t31-t43). Pools of TPC, DOC, and DIC were approximately 420, 7200, and 25â¯200â¯mmolâ¯Câ¯m.sup.-2 at the start of the experiment, and the initial CO.sub.2 additions increased the DIC pool by ââ¼ââ¯7â¯% in the highest CO.sub.2 treatment. Overall, there was a decrease in TPC and increase of DOC over the course of the experiment. The decrease in TPC was lower, and increase in DOC higher, in treatments with added CO.sub.2 . During phaseÂ I the estimated gross primary production (GPP) was ââ¼ââ¯100â¯mmolâ¯Câ¯m.sup.-2 â¯day.sup.-1, from which 75-95â¯% was respired, ââ¼ââ¯1â¯% ended up in the TPC (including export), and 5-25â¯% was added to the DOC pool. During phaseÂ II, the respiration loss increased to ââ¼ââ¯100â¯% of GPP at the ambient CO.sub.2 concentration, whereas respiration was lower (85-95â¯% of GPP) in the highest CO.sub.2 treatment. Bacterial production was ââ¼ââ¯30â¯% lower, on average, at the highest CO.sub.2 concentration than in the controls during phasesÂ II and III. This resulted in a higher accumulation of DOC and lower reduction in the TPC pool in the elevated CO.sub.2 treatments at the end of phaseÂ II extending throughout phaseÂ III. The âextraâ organic carbon at high CO.sub.2 remained fixed in an increasing biomass of small-sized plankton and in the DOC pool, and did not transfer into large, sinking aggregates. Our results revealed a clear effect of increasing CO.sub.2 on the carbon budget and mineralization, in particular under nutrient limited conditions. Lower carbon loss processes (respiration and bacterial remineralization) at elevated CO.sub.2 levels resulted in higher TPC and DOC pools than ambient CO.sub.2 concentration. These results highlight the importance of addressing not only net changes in carbon standing stocks but also carbon fluxes and budgets to better disentangle the effects of ocean acidification.