Berowra Estuary is a eutrophic drowned river valley in Sydney, Australia. The mid region of this estuary has persistently high levels of phytoplankton biomass (>15 - 60 mg.l-1) throughout the austral summer. Tidal flushing, primary production, phytoplankton and zooplankton communities were investigated to establish the processes leading to the blooms. Flushing times varied along the estuary, but were highest (7 days) at the bloom site. Primary production was highest at this site, where flushing times were sufficiently long for nutrients to be taken up and for primary production to occur. Phytoplankton taxa, over the study period were dominated by various species of Chaetoceros, Pseudo-nitzschia, Thalasiosira and Skeletonema. A size based approach, using image analysis technology, was used to investigate zooplankton. Zooplankton biomass (wet weight of taxa between 90-900 mm equivalent spherical diameter) in the bloom area (200 mg.m-3) was significantly greater than upstream (140 mg.m-3) and downstream (120 mg.m-3) sites.. Numbers of individuals in the smallest zooplankton size classes were closely related to phytoplankton biomass. The relationship decreased with increases in the particle size classes, showing an uncoupling between phytoplankton biomass and numbers of larger zooplankton. This uncoupling was probably due to the time needed for somatic growth to occur in the zooplankton. Flushing times in the bloom reach were sufficiently long for secondary production (somatic and egg production) to take place in the zooplankton taxa present during the study. Environmental conditions (nutrients, light intensity and temperature) were such that zooplankton grazing and estuarine flushing were unable to reduce phytoplankton concentrations to below 10 µgl-1.