In a lake basin, there is a mismatch between river and lake water quality targets and a method for setting specific water quality targets for these rivers is urgently needed. Using Dianchi Lake as an example, we proposed a lake basin water quality management system based on the river-lake water quality response relationship, coupled with a Soil and Water Assessment Tool (SWAT) basin hydrological model and Environmental Fluid Dynamics Code (EFDC) lake water quality hydrodynamic model. River water quality control requirements based on the river-lake water quality response were proposed, under the premise that the Dianchi Lake water quality reaches the required standard. Then, water quality control targets for rivers were determined, and corrected for influencing factors, such as current river water quality and composition of flow. Our systematic approach efficiently identified key lake basin pollution sources, and accurately located key points for water quality improvement and pollution control. Combined with a correction for clean water source and current water quality of each river, the proposed water quality targets were practical and operable. Meanwhile, the EFDC model was used to verify the entire process to ensure that river water quality targets could be set to achieve lake water quality targets. To ensure that Dianchi Lake water quality can reach Class IV standard, the Chemical oxygen demand (COD) concentration would need to be maintained under 30 mg/L,Waihai total nitrogen (TN) below 7 mg/L, total phosphorus (TP) below 0.2 mg/L, and ammonia nitrogen (NH-N) below 2 mg/L.