Source water samples and outlet water samples from different treatment processes of the Beijing Ninth Water Works were concentrated in situ with XAD-2 filled columns. GC-MS analysis and toxic assessment including acute toxicity evaluation by luminescent bacterium bioassay(Q67 strains) and mutagenicity assessment by Ames test(TA98 and TA100 strains with and without S9 addition) were conducted on these samples. The results showed that prechlorination caused the direct and indirect frame shift mutagenicity as well as indirect base pair substitute mutagenicity. Addition of coagulant may increase the base pair substitute mutagenic effects greatly. Sand and coal filtration and granular activated carbon filtration could effectively remove most of the formed mutagens. The rechlorination do not obviously increase the mutagenic effects. No mutagenic effect was observed in tap water. Acute toxicity showed the same variation with that of mutagenicity during the treatment processes. Sample from flocculation treatment process was found to be the most toxic sample. Results of GC-MS analysis showed that water in this plant was not contaminated by PCB. Concentrations of toluene, naphthalene and phenol increased in flocculation treatment process and in tap water. However, the concentrations of these substances were at the level of microgram/L, therefore, were not high enough to cause mutagenicity.