Eutrophication is a major problem in China. To combat this issue, the country needs to establish water quality targets, monitoring systems, and intelligent watershed management. This study explores a new watershed management method. Water quality is first assessed using a single factor index method. Then, changes in total nitrogen/total phosphorus (TN/TP) are analyzed to determine the limiting factor. Next, the study compares the eutrophication status of two water function districts, using a comprehensive nutritional state index method and geographic information system (GIS) visualization. Finally, nutrient sources are qualitatively analyzed. Two functional water areas in Tianjin, China were selected and analyzed: Qilihai National Wetland Nature Reserve and Yuqiao Reservoir. The reservoir is a drinking water source. Results indicate that total nitrogen (TN) and total phosphorus (TP) pollution are the main factors driving eutrophication in the Qilihai Wetland and Yuqiao Reservoir. Phosphorus was the limiting factor in the Yuqiao Reservoir; nitrogen was the limiting factor in the Qilihai Wetland. Pollution in Qilihai Wetland is more serious than in Yuqiao Reservoir. The study found that external sources are the main source of pollution. These two functional water areas are vital for Tianjin; as such, the study proposes targeted management measures.