The sub-watershed prioritization is the ranking of different areas of a river basin according to their needto proper planning and management of soil and water resources. Decision makers should optimallyallocate the investments to critical sub-watersheds in an economically effective and technically efficientmanner. Hence, this study aimed at developing a user-friendly geographic information system (GIS) tool,Sub-Watershed Prioritization Tool (SWPT), using the Python programming language to decrease anypossible uncertainty. It used geospatialestatistical techniques for analyzing morphometric and topo-hydrological factors and automatically identifying critical and priority sub-watersheds. In order toassess the capability and reliability of the SWPT tool, it was successfully applied in a watershed in theGolestan Province, Northern Iran. Historical records offlood and landslide events indicated that theSWPT correctly recognized critical sub-watersheds. It provided a cost-effective approach for prioritiza-tion of sub-watersheds. Therefore, the SWPT is practically applicable and replicable to other regionswhere gauge data is not available for each sub-watershed.