The sub-watershed prioritization is the ranking of different areas of a river basin according to their need to proper planning and management of soil and water resources. Decision makers should optimally allocate the investments to critical sub-watersheds in an economically effective and technically efficient manner. 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 any possible uncertainty. It used geospatial–statistical techniques for analyzing morphometric and topo-hydrological factors and automatically identifying critical and priority sub-watersheds. In order to assess the capability and reliability of the SWPT tool, it was successfully applied in a watershed in the Golestan Province, Northern Iran. Historical records of flood and landslide events indicated that the SWPT correctly recognized critical sub-watersheds. It provided a cost-effective approach for prioritization of sub-watersheds. Therefore, the SWPT is practically applicable and replicable to other regions where gauge data is not available for each sub-watershed.