The Songhua River is one of the biggest rivers in China and is the major freshwater source for industry and agriculture, as well as the source of the drinking water for millions of residents living along it. Heavy contamination of the Songhua River is due to domestic sewage and industrial wastewater. Thus, we set out to determine the carcinogenic potential of water samples taken from drinking water source of Harbin city in the Songhua River. Short-term genotoxic bioassays using Ames, SCE, and cell transformation assays were employed to examine the genotoxic activity of the ether extracts of water samples taken from the Songhua River. The results of the Ames test indicated that there were frame shift mutagens in the water samples, which were both direct and indirect. A dose–response relationship for the SCE assay was obtained, and the SCE cumulative frequency moved obviously to the right with increasing doses of water samples. Typical transformed foci were formed in NIH3T3 cells induced by ether extracts of water samples and the transformation frequency showed a dose–response relationship. The transformed cells showed the characteristics of malignant cells. All of the results indicated that the ether extracts of water samples taken from the Songhua River showed genotoxic activity.