Groundwater studies have become of great concern especially in arid and semi-arid areas as they rely heavily on groundwater as a main source. In Egypt there are many aquifer systems of which the Nile Delta aquifer is considered as one of the most important aquifers. However, there are several environmental problems such as salinization, water pollution, logging and mounding of groundwater levels affect the development in eastern Nile Delta region. The region of concern in this study is El-Obour City which is located about 37 km Eastern of Cairo and lies on the hydrologic basin of Heliopolis. It comprises part of the desert area to the east of the Nile delta and covers about 530 Km2. Due to the low permeability of some layers and the leakage from water networks and the seepage from the green areas near to the city the 6th and 7th districts suffered of the groundwater levels rise and logging. Vertical drainage wells were suggested to drain water from the higher layers to the lower layers which have more permeability. However, the optimum number of the drainage wells is one of the big issues in such projects for the practical point of view and for economic purposes. In order to simulate the study area and the existing conditions a simulation package of GMS 7.1 was used. The vertical drainage wells were represented by large vertical hydraulic conductivities with respect to the horizontal conductivities. It was concluded that the ratio of kh/kv should not be less than 0.1, because after this ratio there is no drop in the water level. In order to select the optimum number of wells, five different scenarios have been applied with various numbers of wells (35, 30, 27, 24 and 20 wells). The optimum number for the drainage wells was selected so as to be the minimum number after which the groundwater levels do not change significantly (less than 5 %). Finally, the optimum number of the vertical drainage wells was taken 27 wells to be implemented in this area.