Increasing atmospheric carbon dioxide (CO2) concentrations due to anthropogenic fossil fuel combustion are currently changing the ocean's chemistry. Increasing oceanic [CO2] and consequently decreasing seawater pH have the potential to significantly impact marine life. Here we describe and analyze the build-up and decline of a natural phytoplankton bloom initiated during the 2005 mesocosm Pelagic Ecosystem CO2 Enrichment study (PeECE III). The draw-down of inorganic nutrients in the upper surface layer of the mesocosms was reflected by a concomitant increase of organic matter until day t11, the peak of the bloom. From then on, biomass standing stocks steadily decreased as more and more particulate organic matter was lost into the deeper layer of the mesocosms. We show that organic carbon export to the deeper layer was significantly enhanced at elevated CO2. This phenomenon might have impacted organic matter remineralization leading to decreased oxygen concentrations in the deeper layer of the high CO2 mesocosms as indicated by deep water ammonium concentrations. This would have important implications for our understanding of pelagic ecosystem functioning and future carbon cycling.