The construction of cascade reservoir systems (CRSs) is increasing globally, providing reliable energy and water resources for human social development, while also having significant impacts on the watershed water environment, particularly in terms of nitrogen and phosphorus distribution in the rivers and lakes of these areas. Watershed management authorities urgently need model tools that can comprehensively analyze the sources of nitrogen and phosphorus in CRSs and the nitrogen and phosphorus cycling in lakes and reservoirs. Therefore, this study establishes a model framework that includes a watershed nutrient load model and a hierarchical reservoir nutrient cycling model, validating and analyzing this framework in the Water Diversion Basin from the Luanhe River to Tianjin (WDBLT) in North China, which yields nitrogen and phosphorus substance flows over different time scales. The conclusions show that banning cage culture and curbing point sources improved reservoir water quality, and the internal TP flux serves as a key environmental indicator. This model framework is scientifically sound, easy to operate, and does not require high data demands, demonstrating high practical value for similar water environmental management in CRS.