The Huon Estuary is a major estuary in south-east Tasmania draining a catchment of temperate rainforest and rural/small urban areas. It is also the main waterway for aquaculture in the region, supporting an industry producing Atlantic salmon, mussels, oysters and abalone, with annual production approaching $100 million. Blooms of Gymnodinium catenatum were first recorded in 1986. Since then there have been irregular blooms, sometimes very extensive throughout the estuarine and coastal waters of south-east Tasmania, with resultant closures of shellfish leases and management problems for the Atlantic salmon industry. As part of a large multi-disciplinary study of the Huon Estuary we investigated the phytoplankton dynamics including G. catenatum blooms between 1996 and 1999. The study incorporated conventional estuary-wide surveys as well detailed weekly monitoring at 5 stations, including use of in-situ automated continuous profiling instruments with measurements of key physical and chemical parameters, including temperature, salinity, fluorescence, pigments, and dissolved oxygen. Against a background of small flagellates there were spring and summer diatom blooms and early summer to autumn dinoflagellates blooms. During summer 1996 dinoflagellates were absent; in contrast in summer and again in autumn of 1997/98 and 1998/99 there were extensive blooms of G. catenatum .Between these blooms Ceratium spp. and diatoms bloomed. Intriguing differences between the summer and autumn blooms of G. catenatum were the consistent presence of sexual stages, including resting cysts during the first bloom, but not in the second, suggesting a more significant role for resting cysts in G. catenatum blooms than previously thought. The blooms did not appear to be macronutrient driven, but the physics of the estuary was important. While blooms could develop and be maintained under only weakly stratified water column conditions a stable water column enhanced intense bloom development, and bloom decline was promoted by a large oceanographic event in one case and declining temperatures below 12 degrees Celsius in another. A key to success of G.catenatum within the flushing regimes of the estuary appears to its strong diurnal vertical migration. This study has demonstrated some of the key factors regulating G.catenatum blooms in the Huon Estuary, as well as showing the importance of fine scale continuous monitoring to resolve the details of bloom dynamics.