Employing the full versions of GIS software with its numerous functions to manage case-specific applications is becoming inconvenient for many reasons. A convenient solution that is spreading worldwide to solve this problem is to develop customized tools that use the same GIS concept to meet specific applications. The water resource department in Gaza strip has been facing technical and financial difficulties in using the full GIS versions in managing groundwater resources. Thus, the objective of this paper was to develop a customized standalone GIS-Based ground water quality assessment tool (GWQAT) to be used by the water resources management department in Gaza strip. GWQAT was developed using Microsoft visual basic programming language, a regression mathematical model, map objects, and map files generated from ESRI ARC Info. GWQAT was designed to achieve many functions such as mapping, map overlaying, buffering, charting, soil hydro-geological profiling, and predicting future groundwater quality parameters variations. The simplicity and validity of GWQAT was demonstrated by its application on the groundwater quality parameters in Gaza strip wells with emphasis on chloride concentration.