Pearl River Delta is characterized by the staggered distribution of rivers network and estuarine system, which is different from the other estuaries of the world. The salty water intrusion in this area is also different as the complex hydrodynamic system. At the same time, Pearl River Delta has a large population and active economic activities, the population affected by salty water intrusion is over 10 million, and the affected daily water supply is over 10million m3 . Thus, Pearl River Water Resources Commission of MWR has implemented water diversion for 8 years since 2005, the flow for repelling salty water intrusion can not be less than 1 800m3 /s at the Wuzhou station. Based on the relationship between the salty tide and runoff, this paper made an analysis and put forward a new water diversion scheme based on the drinking water supply target and flow controlling.