Today, the preparation of flood zoning maps is one of the basic and important issues in the study of development projects in the world; it is considered before any investment by the related organizations. In this paper, flood zoning was performed using the two-dimensional model HEC-RAS and GIS in order to assess the risk of the construction of a railway station near the bank of the Iranshahr River, in a range of 2500 meters. Two-dimensional hydraulic application could create a more accurate flow pattern in comparison to the one-dimensional model used in the previous studies, especially in the flood plain areas. In this paper, due to the important role of the topography of the area in ensuring the accuracy of the calculation, a Digital Elevation Model (DEM) was used with very high precision (about 2 meters), as obtained from aerial photos. The results of this study indicated the onrush of flood, depth and flow velocity in different return periods. Based on the comparison of water surface profiles in the floodplains with the return period of 100 and 25 years, the maximum difference between the water levels was 0.5 m, which seemed to be reasonable by considering the low slope of the studied area. The results of this paper, therefore, showed that the location of the railway station was in medium risk and the outskirt of floodplain.