To improve the management of discharge pollutants loads in the reservoirs’ watershed, an approach of the allowable pollutants loads calculation and its allocation, based on the water environment model, was proposed. Establishment of the approach framework was described at first. Under the guidance of this framework, two major steps were as follows: modeling and scenario analysis were involved and should be applied to support the decision of discharge loads management; Environmental Fluid Dynamic Code (EFDC) model was selected as the kernel model in this framework. In modeling step, spatial discretization for establishing cell map in model, data preprocessing, parameter calibration and uncertainty analysis (which is considered as the significantly relevant factor of the margin of safety (MOS)), were conducted. As a result of the research, the model-based approach presented as a combination of estimation and precise calculation, which contributed to scenario analysis step. Some integrated modules, such as scenario simulation, result analysis and plan optimization were implemented as cycles in the scenario analysis. Finally, allowable pollutant loads under various conditions were calculated. The Chaihe Reservoir in Liaoning Province, China was used as a case study for an application of the approach described above. Results of the Chaihe reservoir water quality simulation, show good agreement with field data and demonstrated that the approach used in the present study provide an efficient and appropriate methodology for pollutant load allocation.