Abstract: Flood is one of the natural disasters that leave great deal of financial and human losses every year. Application of levee is among the common flood control measures. Sistan Alluvial Plain is permanently prone to floods because of being situated on the edge of Hirmand Basin and also having negligible ground slope. Increasing of maximal flow rate by levee, using HEC-RAS mathematical model were studied in the present research. For this purpose, the geometrical plan of the river was prepared with the aid of HEC-GeoRAS software and through using regional topography data. After importing the data to HEC-RAS model, flood phenomenon was simulated in different return periods. Results of the current research indicate that Sistan River is not able to transport water at a flow rate exceeding 810 (m3/s); this current is equivalent of flood with recurrence interval of 9 years. To enhance the flood conveyance capacity of Sistan River, levee structure was applied. The results show that using levee increased river’s conveyance capacity up to the flow rate of 1700 (m3/s) which is equivalent of a recurrence interval of 107 years. Therefore, application of levee on Sistan River can favorably mitigate the risks resulting from flooding in Sistan Plain.