The Choghakhor International Wetland plays an important role in preserving and protection of part of the plant and animal species in the Iranian plateau. Since the water of this wetland is utilized for different human purposes, complete periodic chemical and physical quality assessment of its water seems necessary. Water quality index (WQI) was calculated using the following eleven parameters: Nitrate, Nitrite, Ammonium, Alkalinity, Hardness, Turbidity, Conductivity, Dissolved Oxygen, Total Dissolved Solid, pH and Biochemical Oxygen Demand (BOD5). For this purpose, the relative weight assigned to each parameter ranged from 1 to 4 based on the importance of the parameter for aquatic environment and human health. The analyses of variance (ANOVA) of data revealed significant differences between different periods of sampling (p<0.01). Therefore we assigned the results in two categories: very poor and inappropriate, which make it not suitable for human uses such as drinking. The most important factor in assessment of water quality in this study was BOD5. The result of this research demonstrated that this method can be used for assessment of water quality in wetlands.