Taihu Lake, the largest freshwater shallow lake in eastern China, has suffered from severe eutrophication over the past two decades. This research developed a three-dimensional eutrophication model to investigate the eutrophication dynamics. The model fully coupled the biological processes and hydrodynamics, and also took into account the effects of sediment release and the external loads from the tributaries. After sensitivity analyses, the key parameters were defined and then calibrated by the field observation data. The calibrated model was applied to study the seasonal primary productions and its regional differences. The comparisons between model results and field data in year 2000 indicated that the model is able to simulate the eutrophication dynamics in Taihu Lake with a reasonable accuracy. From the simulation experiments, it was found that the meteorological forcing have significant influences on the temporal variations of the eutrophication dynamics. The wind-induced circulation and sediment distribution play an important role in the spatial distribution of the algae blooms.