As the largest inland drainage lake in China, Lake Bosten plays a critical role in water resource allocation and ecological barrier functions in arid regions. However, the continuous exceedance of the chemical oxygen demand (COD) concentration standard in the lake in recent years has become a prominent issue in regional ecological and environmental governance. This study using the three-dimensional hydrodynamic and water quality model Environmental Fluid Dynamic Code (EFDC) for Lake Bosten. Combined with scenario simulation methods, we systematically reconstructed the dynamics of hydrodynamic conditions and COD concentrations in Lake Bosten from 2014 to 2023. Multiple hydrological regulation scenarios were constructed to evaluate the improvement effects of different measures on the lake’s hydrodynamic conditions and COD concentrations. The results show: 1) Changes in COD concentration in Lake Bosten result from the combined effects of natural processes (high evaporation, low flow velocity, long water residence time) and human activities (reed cultivation areas); 2) The lake exhibits weak hydrodynamic conditions with a west-high-east-low pattern, and effectively enhancing lake-wide hydrodynamic conditions is key to improving COD concentration; 3) The “Kaidu-to-Huangshui Water Diversion” scenario can significantly improve lake hydrodynamics by reallocating inflow, and can reduce COD concentration by 18.37%, making it the optimal regulation scheme. This research can provide a scientific basis for COD control in Lake Bosten and offer insights into pollution management and water quality governance in arid-region lakes.