Sampling was conducted at three site groups, group E (in East Taihu Bay), G (in Gonghu Bay) and M (in Meiliang Bay) in Lake Taihu. TN and TP concentrations among site groups was in the increasing order of E < G < M. TP level at G sites is at the critical threshold for loss of submersed macrophytes. Mean values of DO and Transparence showed different trend, i.e., E > G > M. The mean phytoplankton fresh-weight biomass at M sites was 5.81 mg/l, higher than that at E sites (4.96 mg/l) and G sites (5.18 mg/l). Mean zooplankton fresh-weight biomass was in the decreasing order of M (6.4 mg/l) > G (4.9 mg/l) > E (2.7 mg/l). However, Rotifera density was in the sequence of E > G > M. Both zooplankton biomass and phytoplankton biomass increased with the rise of TN and TP concentrations. Relationships between zooplankton biomass and phytoplankton biomass showed that zooplankton played a limited role in the control of algae in eutrophic lakes. Nutrient availability is much more important than zooplankton grazing pressure in controlling phytoplankton growth in lakes. For most sites in Lake Taihu, reduction of nutrient loading, as well as macrophyte conservation, zappears to be especially important in maintaining high water quality and regulating lake biological structure, but for M sites, it's urgent to control nutrient inputs rather than to restore macrophyte community.