Organic pollutant ingredients and content of water samples from Taihu Lake were analyzed by GC-MS. Results showed that Taihu Lake was already contaminated by the organic pollutant, and 15 kinds of targeted organic pollutants were detected. At lower concentrations (1 time), organic pollutants could not have notable effect on the growth of Euglena gracilis, but could increase the content of photosynthetic pigment. At higher concentrations (5, 10 times), organic pollutants restrained the growth of E. gracilis remarkably, and decreased the content of photosynthetic pigment. Activities of SOD and POD increased with the content of organic pollutants. It is indicated that organic pollution could induce activities of antioxidation enzymes in E. gracilis. TOM and TM for the genotoxicity assay increased and DNA damage was found. In higher concentration groups, DNA damage was serious and had an obvious dose-effect relationship. It is indicated that Meiliang bay water may have potential mutagenicity. Comet assay combined with SOD analysis was of value to genotoxic monitoring of polluted water and was a suitable biomarker for organic pollutants in water.