Long-term phytoplankton assemblages in a large shallow Chinese lake, Lake Taihu, were presented using the monthly monitoring data from October 1991 to December 1999. Earlier research results (1960, 1981 and 1988) were applied to discuss the different trophic stages of the lake. The species composition in the lake was more closely related to eutrophication level than to lake-size, shallowness, or turbidity. Each summer, a single peak of phytoplankton biovolume appeared in Meiliang Bay. The results of principal components analysis showed a distinct temporal shift in species composition between summer and winter. A clear spatial difference in phytoplankton occurred between Meiliang Bay and the lake centre. Wind speed and direction affected the horizontal distribution of phytoplankton, especially Microcystis, in the lake. Temperature, underwater light climate, nutrients and grazing by zooplankton and by fish were discussed to explain the overwhelming dominance of Microcystis. Four nutrient-phytoplankton stages were identified in the lake: an oligo-mesotrophic stage with low algal biomass until 1981, a eutrophic situation with blooms of Microcystis during 1988–1995, hypertrophic conditions with the dominance of Planctonema and total phosphorus up to 200 mg m−3 from 1996 to 1997 and the restoration period after 1997. The wax and wane of the phytoplankton assemblages were mainly controlled by temperature, wind and turbidity while long-term biomass dynamics were influenced by the level of nutrients.