As the first stop that "Water diversion from Yangtze River to Lake Taihu" project water flowing into, Gonghu Bay is the base place to evaluate the water ecological environment changes in response to the project. In this paper, a short-term water diversion in summer in Gonghu Bay is investigated. The physical and chemical indicators and phytoplankton community of the two monitoring water samples before (July 24, 2013) and after short-term water diversion (August 18, 2013) is compared and analyzed, and then the relationship between phytoplankton community and environmental factors is analyzed. Our results showed that the short-term water diversion in summer had a significant effect on the water quality in Gonghu Bay. After short-term water diversion, the pH value of the water body in the monitored area decreased slightly. The values of turbidity, dissoved oxygen (DO), nitrate nitrogen (NO₃^--N), total nitrogen (TN), total phosphorus (TP) and permanganate index (COD_Mn) in the monitoring area during the water diversion were higher than those before water diversion. The most significant area affected by the water diversion was the entrance to Gonghu Bay of Wangyu River and the middle area of Gonghu Bay. Dominant genus of algae is still microcystis, while the proportion of cyanobacteria species decreased and non-blue algae species such as green algae and diatoms increased. Affected by the water diversion, Shannon-Wiener diversity index and Pielou evenness index in the entrance to Gonghu Bay of Wangyu River and the middle area of Gonghu Bay were increased as well. However, the short-term water diversion in summer didn't significantly affect the algal community structure in the middle area of Taihu Lake. Meanwhile, the redundancy analyses of phytoplankton community structure and environmental factors by the use of CANOCO software showed that the pH, DO, NO₃^--N, TN TP and COD_Mn were significantly correlated with the distribution of phytoplankton community in Gonghu Bay of Lake Taihu, which were the main environmental factors influencing the phytoplankton community.