Urbanization refers to a process in which an increasing proportion of an entire population lives in cities and the suburbs of cities and/or change of land use from agriculture to human settlements, commercial sectors and industries. Regarding the groundwater resources, the imposed of contaminant load to groundwater is one of the main space-time issue in the urbanization process. In the last two decades, urbanization has been transformed Yogyakarta City – Indonesia to beyond its administrative area with about one million inhabitants and without proper access to water supply and sanitation system. About 70% of the city population depends on the shallow groundwater aquifer for much of their water supply. In order to recognize the issues of groundwater deterioration due to the improper urbanization condition in the Yogyakarta City, study of groundwater vulnerability, potentialcontaminant load and groundwater quality are carried out and new predictive relationship is derived for the assessment of the groundwater contamination hazard. Finally, the risk and protection priority as well as the possible management measures are determined to rectify the groundwater contamination problem and to encourage the sustainable use of the shallow groundwater resources beneath Yogyakarta City.