In addition to its environmental effects, Karoon River plays an important role in the neighboring people's lives. In recent years, its salinity has been raised due to low flow rates and increased loading of pollutants. One of the practical issues in this regard is the management of salinity sources considering different applicable scenarios. The aim of this study is evaluating these management scenarios by removal and reduction of point source pollutants loading. The hydrodynamics and salinity of this study, from Molasani to Farsiat stations, were simulated using MIKE11 model. Continuing the existing conditions revealed that loading pollutant sources will lead to an increase in salinity longitudinal profile, where Ahvaz and farmlands are located. The outcome of the removal scenario shows that eliminating agricultural sources in the dry season and the industrial and urban sources in the wet season dramatically results in river salinity reduction upstream and downstream of Ahvaz. Also, results expressed that upstream boundary reduction shows influence at the end of the study area with an average salinity reduction of 35.10 and 26.10%, in the wet and dry seasons, respectively. The simulation results of combined scenarios show that managing the loading of pollutant sources through the upstream boundary is of significant importance.