The Qiyeshi Reservoir, located in Dongguan City, Guangdong Province, is a medium sized reservoir for drinking-water supply. To meet the demand in water quantity and water quality, the water was diverged from Dongjiang River to the reservoir in October 2002. In order to understand the ecological effect of this water diversion, the hydrologic conditions, water quality and the distribution of phytoplankton assemblage were surveyed from 2003 to 2004. The results showed that the Total phosphorus (TP) concentration was remarkably diluted by water flushing, however, total nitrogen concentration (TN) only decreased in the flood seasons. In flood seasons, the improvement of light condition in water favored phytoplankton growth, leading to the increase in phytoplankton abundance and biomass. In dry seasons, phytoplankton abundance decreased largely due to the dilution by huge amount of transported water into the reservoir. The water diversion also had an impact on species composition of phytoplankton. The species number increased notably, especially for chlorophyta. Pseudoanabaena sp. and Dactylococcopsis continued to be the dominated species, however, Achnanthaceae and Synedra sp. became one of the dominated species, and the abundance of Phacus stokesi and Trachelomonas sp. decreased remarkably.