Qingcaosha reservoir is a newly establishedimportant reservoir located at Yangtze Estuary of China.The aim of this study is to investigate microbial community structure and its shift associated with different water quality during test running period of Qingcaosha reservoir The results showed the concentrations oftotal nitrogen(TN)and total phosphorus(TP)in Qingcaosha reservoir were lower than that of Yangtze estuary.