Genotoxicity of substances is unknown in the water after treatment processes. Genotoxicity decreased by activated carbon treatment but increased by chlorination. Halogenated hydrocarbons and aromatic compounds contribute to genotoxicity. Genotoxicity was assessed by umu test; acute and chronic toxicity by ECOSAR. Inconsistent results confirmed that genotoxicity cannot be assessed by ECOSAR. Advanced water treatment is commonly used to remove micropollutants such as pesticides, endocrine disrupting chemicals, and disinfection byproducts in modern drinking water treatment plants. However, little attention has been paid to the changes in the genotoxicity of substances remaining in the water following the different water treatment processes. In this study, samples were collected from three drinking water treatment plants with different treatment processes. The treated water from each process was analyzed and compared for genotoxicity and the formation of organic compounds. The genotoxicity was evaluated by an umu test, and the acute and chronic toxicity was analyzed through Ecological Structure- Activity Relationship (ECOSAR). The results of the umu test indicated that biological activated carbon reduced the genotoxicity by 38%, 77%, and 46% in the three drinking water treatment plants, respectively, while chlorination increased the genotoxicity. Gas chromatograph-mass spectrometry analysis revealed that halogenated hydrocarbons and aromatic compounds were major contributors to genotoxicity. The results of ECOSAR were not consistent with those of the umu test. Therefore, we conclude that genotoxicity cannot be determined using ECOSAR .