To understand the influence of flow speed on algae growth rates in reservoirs, in situ experiment using stirring experimental tank was carried out in different water level periods (low water level and high water level) in Pengxi River backwater area, a tributary of the Three Gorges Reservoir. Four different treatments, i.e. flow speeds of 0, 0.1, 0.2 and 0.3 m/s, were selected in the experiment. In summer low water level period, light and temperature conditions were feasible for the growth of algae. Increase in flow speed (>0.2 m/s) would have significant impacts on the growth of algae. In general, relationships between algal growth rates and flow speeds were in accordance with logarithmic function. In winter, a high water level period, increasing in flow speed would increase in turbulence in water column, preventing sedimentation of algae. In this period, regulating flow speed and discharge to control algal growth might be difficult.