To ensure the safety of the water supply of the Panjiakou reservoir, in 2016, the Chinese central government comprehensively banned the fishing cage culture that had lasted for almost 30 years. However, the long-term effects and retention impacts of the government’s mandatory intervention on the reservoir water quality are unknown. To determine the reservoir water quality, we employed statistical methods along with the mathematical model to investigate the internal relationship since the construction of the reservoir. We applied seasonal trend decomposition using loess (STL) to explore the long-term and seasonality trend of monthly total nitrogen (TN) and total phosphorous (TP). To separate the impact of upstream water quality changes from cage culture on reservoir water quality, we employed generalized additive models (GAMs). We created a model, the LAKE2K model, to investigate the internal sources of the sediment that accumulated during the aquaculture period and its retardant effect. The results revealed that the concentration of upstream TN was more affected by non-point sources than by TP. The long-term policy of encouraging aquaculture has greatly contributed to the increase in the reservoir TP concentration rather than an increase in TN; the prohibition of cage aquaculture has resulted in a sharp drop in TP. After the ban, the sediment became the main source of TP. We suspect that the TP concentration of the reservoir and sediment will decrease gradually until a new equilibrium is reached within 10 years. This study offers lake managers an opportunity to increase their insight into the interaction of management measures with water quality and provides valuable information for the natural recovery of the eutrophic system.