Every year, waters on earth receive large quantities of wastewater from industry, agriculture, fish and poultry raising, and municipal sewage treatment plants. Consequently, the aquatic environment on the earth is under a serious challenge from a very large quantity of pollutants such as antibiotics, insecticides, herbicides, hydrocarbons, etc., contained in the domestic wastewater, industrial and agricultural waste water and illegal effluents. In particular, with the development of intensive aquiculture and poultry, the effluent pollution has recently become more and more serious with more attentions. Furthermore more and more chemical pollutants discharged into aquatic environment have been detected with the advancement of analytical techniques. These chemicals can cause toxic effects on water habitats after discharged into aquatic environment. However, microorganisms have many key functions in pollution control. In this review, applications of microorganism in the degradation of chemicals in aquatic environments are reviewed. It was concluded that most applications of microorganisms degrading chemicals focused on aquaculture waters, whereas other aquatic systems (such as river, lake, sea, coastal waters) have been scarcely studied.