Due to water scarcity, it is important to organize and regulate water resources utilization to satisfy the conflicting water demands and needs. This paper aims to describe a comprehensive methodology for managing the water sector of a defined urbanized region, using the robust capabilities of a Geographic Information System (GIS). The proposed methodology is based on finding alternatives to cover the gap between recent supplies and future demands. Nablus which is a main governorate located in the north of West Bank, Palestine, was selected as case study because this area is classified as arid to semi-arid area. In fact, GIS integrates hardware, software, and data for capturing, managing, analyzing, and displaying all forms of geographic information. The resulted plan of Nablus represents an example of the proposed methodology implementation and a valid framework for the elaboration of a water master plan.