In Semarang, which is located on the northern coastal Java (Central Java Province), the number of registered deep wells increased tremendously in the 1980s. Therefore, there is an urgent need to give a quantitative assessment to the actual situation. This study focused on major improvements to the existing hydrogeological model by using integrated geological, hydrogeological, and hydrological data. The hydrogeological model was then implemented into a numerical model to simulate groundwater flow under steady state and transient conditions. The calibrated transient model was applied for several prognoses in order to predict groundwater levels and storages based on the future city development and climate change. The research was divided into three main sections: understanding the natural system, developing the hydrogeological model (conceptual model), and finally applying the numerical groundwater flow model. Two aquifers (Aquifer 1 and Aquifer 2), three aquitards (Aquitards 1, 2, and 3) and one aquiclude are distinguished as HSU in the study area. The potential groundwater recharge has a range from 70 to 410 mm/yr. The calibrated steady state model conducts a reasonable value of abstraction around 60 MCM/yr with a real groundwater recharge of about 43% of the potential groundwater recharge (30–176 mm/yr). The transient model simulates groundwater flow from 1998 until 2010. The model results show a decrease of piezometric heads in the north of Semarang year by year due to an intensive abstraction. Prognoses using the transient model indicate that a reduction of the annual abstraction by
20 MCM/yr until 2031 is necessary to restore groundwater resources in Semarang urban area and to prevent a further drawdown of groundwater levels.