Flows of carbon and nitrogen in a natural phytoplankton assemblage from the plume of the Scheldt estuary were followed during and after a light-induced bloom by measuring changes in concentrations and stable isotope ratios in mesocosms after addition of 13C (as bicarbonate or glucose) and 15N (as ammonium or nitrate). Addition of 13C-bicarbonate showed a strong coupling between algal primary production and bacterial secondary production, while addition of 13C-glucose revealed bacteria as a carbon source for eukaryotes. Tracing the 13C into mesozooplankton, we identified selective grazing on algae during the phytoplankton bloom, transfer of carbon from bacteria to mesozooplankton and opportunistic feeding strategies after the bloom. Nitrogen labeling confirmed carbon labeling findings, identified bacteria rather than mesozooplankton as ammonium regenerators and allowed quantification of nitrification.