Abstract: The water pullution and its toxicity to fishes in the areas of Anqin, Nanjing, Zhenjiang and Changjiang estuary along the Yangtze River were being investigated. The results indicated that the water quality of the main channel was up to the state grade 2 standard for surface water. But the water quality along the river bank was mainly polluted by petroleum hydrocarbons and volatile phenol . These contaminants were toxic to fishes at a certain degree. They not only induced the acute toxicity to fishes, but also caused heightened percentage the micronucleus in fishes. High accumulations were found in fishes in the above mentioned river areas. It has showed that the lower reaches of the Yangtze River are polluted by the industrial effluent and the fishery in these areas affected by the pollution.