Heavy metal distribution in aquatic ecosystems can be influenced by a variety of factors. In this study, the spatial distribution and seasonal variation of heavy metals (Cd, Ni, Cu, Zn, Cr, and Pb) in lake water and sediments of different lake zones of a large, shallow, eutrophic freshwater lake, Taihu Lake, were investigated. Metal concentrations in the river water, bloom assemblages, and macrophyte materials were also determined. The results demonstrated that metal distribution in Taihu Lake showed distinct patterns in different seasons. Metal concentrations in rivers around Taihu Lake showed some peaks that may contribute to the elevated metal concentrations in lake water and sediments. However, the metal concentrations in the river water did not fluctuate significantly with months (March, July, and December). The dissolved metal concentrations in the phytoplankton-dominated zone of the lake were significantly higher than those in the macrophyte-dominated lake zone in summer, which could be attributed to the different dominated primary producers in the two lake zones. Statistical analysis results demonstrated that the dissolved metal concentrations were positively correlated with water turbidity for all metals in July. However, the positive correlations disappeared for most metals of March and December samples. The results of this study could provide useful information for further understanding of the transportation and fates of heavy metals in different freshwater lake ecosystems.