The use of fertilizers in agriculture in Egypt, especially nitrogen, has increased significantly in the last decade, resulting in nonpoint contamination of the groundwater resources. This study investigated the effect of using nitrogen fertilizer on groundwater contamination with nitrate in the central southern part of the Nile Delta. NO3− concentrations in shallow groundwater were assessed based on the applied urea dose (the common nitrogen fertilizer used) in year 2014. A groundwater modeling system (GMS) comprising MODFLOW and MT3D was used to simulate the three-dimensional groundwater flow and NO3− transportation processes in El-Menoufia Governorate, located in the central region of the Nile Delta aquifer. Calibration for MODFLOW was conducted to match known head configurations to minimize the water balance differences. Calibration of MT3D was accomplished by fitting the model to the measured NO3− concentrations during the year 2014. The results highlighted areas of groundwater contamination by NO3−, which occurred at shallow depths (40 m) due to the significant loads of nitrogen fertilizer application and the flood irrigation method. While the results suggested one approach was to avoid using contaminated shallow groundwater as a water source, a more sustainable approach would be to implement best management practices to reduce and control the amount of nitrate leaching into the shallow groundwater system in the future.