The systematic data management system in the area of river flow analysis has not yet constructed, even though the need is evident due to the complicated process of tremendous input/output data in the modeling study and the importance of visualization of spatial flow variation. The objectives of this study are to suggest the method for analysis of changing river sections affecting ecological habitat characteristics. The effects of ecological habitat characteristics are assessed with respect to changing river sections. A GIS special analysis is created representing in the past section of Nonsan-river using historical data. Topographic surfaces are subject to erosional and depositional forces that a specific set of surface characteristics unique to elevation data. GIS spatial analyst is used to generate surface grids from historical point data. Using the GIS spatial analyst can be constructed sections for anywhere of river. The change of depth between 1979 and 1988, the left bank elevations of a river are increased about 1.5m. But the right bank elevations of a river are decreased about 2.3m caused by erosion. In addition, the change of spatial between 1988 and 2002, the regions of a river from upper stream to midstream are decreased the elevation. But the downstream regions are increased the elevation. These changes are analyzed in GIS program to assess methods for affecting ecological habitat.