Taihu Lake is the third largest freshwater lake in China. Taihu Basin is one of the most densely populated and urbanized areas in this country. This area provides 15% of the GDP. Meiliang Bay is located in the north part of the Lake. It provides the municipal water source for Wuxi City. Some parts of the lake have been found to be highly polluted due to eutrophication for over a decade. Surface water (0-0.5 m) samples were collected from the Meiliang Bay by the aid of Global Position System (GPS) for positioning. Water samples were concentrated 5000 times with XAD-2 resin columns. A reverse mutation test using histidine-dependent Salmonella typhimurium strains was employed to assay the genotoxicity of the samples. The results showed that the sample from position 6 had the highest genotoxicity either in the case of activating with eucaryotic S9 system or without S9. The genotoxic effect included, at least, two different molecular mechanisms: nucleotide point substitution on DNA molecules and reading frame shifting caused by nucleotide insertion or deletion. The genotoxicity of the water body in Meiliang Bay, Taihu Lake should be kept in close monitoring.