In this study, we examined possible impacts of the Yangtze River Three Gorges Dam (TGD), the world largest hydroelectric construction, on the adjacent marine ecosystem of the East China Sea (ECS) during its initial water storage period. The TGD filled the first one-third of its storage capacity of 39 billion m3 in 10 days in June 2003, causing an abrupt reduction in the river flow into the ECS. Noticeable changes in the microbial community structure including pico-sized autotrophs, heterotrophic bacteria and microbial diversity in the estuary and the ECS were observed 2 months later. Although causes for these changes could be multiple, the sudden decrease of river runoff and an ensuing intrusion of ECS ocean currents were postulated to be among the major ones.