The macro water system flows in nature based on the physiographic condition of watershed and it is not limited to by a political border. In order to achieve water governance and rational use of natural resources, water resources must be managed at the watershed scale and under climate governance. But in most areas where urbanization has grown based on political borders, they mistakenly reduce the water system to the same range of political borders, which causes disruption in a chain of ecosystem relationships and complexity in water resources management. This issue has historical roots and originates from insufficient knowledge and technological limitations in the past era and when Political borders were formed. But in the current era, due to the advancement of technology and the use of Geographic Information Systems (GIS), as well as the increase in human knowledge about the inherent complexity of the water system, it has been possible to link the political boundaries with the boundaries of the watershed by producing and presenting new maps. Research literature shows that water resources and other environmental goods are better protected in countries where political borders and watershed borders are more compatible. Therefore, in the current study, by using the geographic information system, the border construction patterns in the country's watersheds have been analyzed. The results of this research show that matching political borders with watershed borders is a necessary step for the governance of Iran's water resources and sustainable development.