Abstract: In order to understand how waterweed and the waste in rivers influence flow in pumping stations, we analyzed the discharge change in four pumping stations of Jiangdu water control project during main flood seasons according to the measured data from the pumping stations since its construction. The results showed that: (1) Before 1983, the discharges in four pumping stations were not affected. The relationships between water level and discharge of four pumping stations were stable. However, since 1987, the discharge decreased when the station pumping time was long. Hence, new water level-discharge relationship should be formulated respectively. (2)When pumping water from the Yangtze River, the waterweed and waste in rivers had the same influence on the discharges in four pumping stations. However, when drainaging water from the Lixia River, the discharge of the fourth pumping station near the Xintongyang River mouth was the largest, whose reduction was the greatest among four pumping stations. (3) In recent years, the longer the operation time of pumping water from the Yangtze River was, the greater the reduction in discharge was, and the flow reductiong phenomena is more obvious when draining water from the Lixia river. These results are meaningful for flood control and drought relief, project safety operation of and water resources planning and management.