Corresponding editor: John Dolan The biomass, production and consumption of phytoplankton, bacteria and zoo-plankton in a shallow Danish estuary (Limfjord) were analysed during a 9-day period. The water column changed between stratified and mixed conditions which influenced the dominant processes in the pelagic system. During strong stratification, phytoplank-ton was mainly controlled by microzooplankton grazing. A mixing event, which homogenized the water column, possibly provided food to a mussel-dominated benthic community. Concomitantly, zooplankton feeding and reproduction decreased. However, the nutrient input to the upper part of the water column during mixing and the subsequent stabilization provided the ideal conditions for the recovery of phytoplankton from the loss processes from previous days. Microzooplankton, which was also a significant consumer of bacteria throughout the sampling period, was not the only consumer controlling phytoplankton. The microbial food web was an important route for total plankton carbon during the study. However, the shorter food web increased in importance during mixing, possibly due to stronger benthic–pelagic coupling than during stratified periods. Stratification-mixing cycles, occurring during short-time periods, should be a key mechanism maintaining the benthic and pelagic communities in this shallow water system.