The influences of tracer type, tracer dosage, tracer monitoring and flow monitoring on water flow connectivity of drinking water source were examined systematically. Electrical conductivity was taken as a reference index to optimize the sampling and flow measurement frequency, and nitrate of potash as the tracer indicator of calculating tracer recovery rate. In association with flow measurement data, a method of quantifying the water system connectivity was proposed to reveal the distribution of groundwater resource. The method was applied to investigate the contradiction between domestic water use and production water use in the provincial boundary of Yeniuyan between Hunan Province and Guangxi Zhuang Autonomous Region. Results unveil that all the water from Yeniuyan flows into the Luoshuidang, and then divided into east and west streams. The east stream flows into the underground river through the Xingfu dam and the Xingfu power station, and finally into the Jiangyuan, while the west stream stretching over 30 km flows into the underground river through the Wuxing tunnel, Wuxing power station and Xingfu power station, and finally into the Jiangyuan. Under the hydrometeorological conditions during the test period, the water diversion of the east branch (Xingfuba) accounted for about 34.9% of the water inflow into the Luoshuidang from Yeniuyan, and that of the west branch (Wuxing tunnel) occupied 65.1%. No connection between Baiquan, Dashuibu, Qingtang, Zhaojiangdong 1 and Zhaojiangdong 2 and Yeniuyan was observed. The trend of groundwater and the proportions of runoff and water diversion were made clear, and the variation characteristics of water volume along the river course were obtained. The research finding is expected to offer technical support for solving such water use disputes and can be used as a reference for analyzing complicatedly connected water system.