Abstract: The recharging sources of river and reservoir type of drinking water sources in Zhuhai City are mainly from Xijiang River, among which the water storage of reservoir type of water sources is mainly supplied by pumping stations from Xijiang River. Cluster analysis and discriminant analysis were used to analyze the characteristics of spatial and temporal distribution of water quality in drinking water sources, so as to discuss the influence of water season change and water sources location on water quality. Water retention time calculation and correlation analysis were used to preliminarily study the influence of water resources allocation and hydraulic retention time on water quality. The result shows that the source water quality in Zhuhai City could be divided into three categories: upstream river type, downstream river type and reservoir type. The concentrations of total phosphorus, fecal coliform, sulfide and nitrate in reservoir type of water sources were lower than those in river type of water sources. The total phosphorus concentrations in the reservoir and river types of water sources were 0.01-0.04 and 0.04-0.12 mg/L, respectively; and the nitrate concentrations were 0.006-1 and 0.100-2 mg/L, respectively. The river type of water sources in the upstream were less affected by the salt tide. The concentrations of sulfate and chloride of river type of water sources in the downstream increased significantly in the dry season, and the water quality of the water source of the downstream in the wet season was similar to that of the upstream. Based on the above analysis result, water resources allocation measures are proposed: Firstly, the self-purification function of reservoir type of drinking water sources could be utilized by extending the hydraulic retention time, including increasing the utilization rate of the reservoir with large capacity and adjusting the connection mode between reservoirs and pumping stations. Secondly, the salt tide resistance function of upstream river type of drinking water sources could be utilized to ensure water salinity meeting the standard in the dry season. Lower cost advantage of downstream river type of drinking water source could be utilized and the water utilization proportion could be increased in the wet season. Furthermore, the pumping stations with lower total phosphorus and nitrate concentrations (such as total phosphorus concentration reaching the standard limit value of type Ⅲ of lake-reservoir type water sources) and closer to the urban area were preferentially selected for water supply. Through the implementation of the above measures, the consideration of water quality factors in water resource allocation is improved, and the impact of water resource scheduling on water quality and the risk of water quality exceeding standard are reduced.