Only few studies were conducted to assess genotoxicity of centralized source waters in China and almost none of them dealt with the causal relationship between the genotoxic effect and genotoxicants. In this work, 16 centralized source waters in China were sampled from five river systems and genotoxicity of their organic extracts was assessed by use of the SOS/umu test for DNA-damaging effect and the miniaturized flow cytometry-based micronucleus (MN) test for chromosome-damaging effect. In addition, initial identification of potential genotoxicants for the six samples from the Yangtze River was done with a GC/MS method and the QSAR toolbox 3.0. The results demonstrate that eight samples showed both indirect and direct DNA-damaging effects, another four samples showed only indirect DNA-damaging effects, while chromosome-damaging effects were found for 14 out of the 16 samples, in which aneugenic and clastogenic modes of action were found for 4 and 10 samples, respectively. Both direct/indirect DNAdamaging effects and chromosome-damaging effects were induced by the six Yangtze River samples, and the existing different types of genotoxicant confirmed the results. Furthermore, o-phenylphenol was initially identified as the major cause for the DNA-damaging effects while PAHs, pesticides, phenol and anthraquinone were identified as ubiquitous chromosome-damaging agents among these samples. In conclusion, a combination of the SOS/umu test and the miniaturized flow cytometry-based MN test to detect both DNA-damaging and chromosome-damaging effects could be used as a comprehensive genotoxicity assessment tool for the evaluation and classification of genotoxicity of complex mixtures, and potential genotoxicants can be initially identified with additional information from chemical analysis and the QSAR toolbox.