Water is an important element and plays a vital role in the formation and survival of natural, economical and social systems in dry climates. Thus, there is a significant necessity to present an optimal method for utilization of water resources in these regions. Constructing dams has been a prevalent method for exploitation of water shed resources for a long time which has positive and negative impacts on the environment. Marvast dam in Yazd province-Iran with the aim of supplying agricultural water in Marvast desert and preventing groundwater loss is studied in this paper. Environmental Impact Assessment (EIA) with two methods of Checklist and ICOLD matrix has been used as a tool to study and decrease the above mentioned impacts. In this method, it was attempted to implement the practical and quantitative models such as estimating the rate of Sedimentation, Flood, Stratification, and Eutrophication. Based upon achieved results and mentioned models, it was recommended to use a combined method to utilize the water resources in Marvast desert. In this method that has major elements including surface waters, ground waters and agricultural wells, the plan for exploitation of water resources is dependent on water input to dam reservoir, region’s irrigation calendar, cultivated land of region, and aquifer surface. This method would result in less negative environmental impact in addition to up to 96.1% increase in irrigation output.