Chagan Lake serves as an irrigation storage reservoir for the Qianguo Irrigation Area and an important ecological barrier in western Jilin. The coupled TUFLOW-FV and Aquatic Ecodynamic (AED2) models were used to simulate the hydrodynamic and water quality of Chagan Lake, and propose the water diversion scheme that could improve the water quality to reach Grade III and maintain the ecological water level. The simulation results showed a satisfactory agreement with observations. The total carrying loads of NH3-N, total nitrogen (TN) and total phosphorus (TP) for Chagan Lake were 1,147.6, 3,686.2 and 100.8 t from May to October. The range of the minimum amounts of water diversion to keep the water quality as Grade III and maintain the maximum ecological water level of 131.5 m for TN, TP were separately [32.60, 49.84, 57.19, 63.70, 70.91], [117.25, 135.26, 168.17, 190.65, 218.32] million m3 and the corresponding reduction amounts of farmland drainage for TN, TP were separately [4.03, 0, 0, 0, 0], [73.08, 61.88, 50.23, 40.94, 31.98] million m3 under the rainfall guarantee rates of 10%, 20%, 50%, 75%, 90%, respectively. The simulation results provide a scientific basis for the water quality improvement and ecological water supplement required for the interconnected river–lake system network (IRLSN) in Western Jilin Province.