Rivers have been addressed as one of main resources of water supply for different consumptions including agriculture, drinking and industry. Therefore, with regard to recent droughts, also rural and urban development, monitoring the quality of these resources is considered as an important function in the context of environmental management. With respect to the importance of Godarkhosh river, located in Ilam province, its entrance into Iraq country, its removal for different consumptions, also discharging various pollutants into this river, its qualitative assessment seems necessary. On the one hand, zoning, contamination and presenting proper image of qualitative condition of surface water by means of GIS resulted into the situation that every management decision that affects directly or indirectly on national surface waters, must be made consciously. Research method is cross- sectional descriptive. It's various stages are including: sampling 10 stations across the river during 6 months (From September 2010 to march 2011), measuring such qualitative parameters as temperature, measuring such qualitative parameters as temperature, dissolved oxygen (O2), essential biochemical oxygen, fecal coliform, Nitrate, phosphate, turbidity, pH, total dissolved solids and data analysis by using national water quality index (NSFWQI). To prepare water qualitative zoning model of this river, besides above index in relation to natural factors, (geology, soil quality, vegetation and local permeability). GIS software was used to consider this model. Obtained results indicated that mean NSFWQI in the best condition with the effect of natural factors is related to stations 5 and 7 with 50/33 and 59/33, respectively. Actually this would determine intermediate condition in regard to qualitative index and average index in worst state with the effect of natural factors is related to station 4 with 49/33 that indicated the appearance of bad qualitative condition.