The multi-aquifer system of the Nubian aquifer in central Sudan hydrogeological system was simulated using a three-dimensional steady-state model. The goal of the study is to detect the effect of pumping on the groundwater flow and thus, the aquifer productivity. The conceptual model of the study area was built based on the available geological and hydrogeological data guided by geophysical survey. Processing MODFLOW numerical code was used to calculate the hydraulic head and water balance under the existing boundary conditions. The model accurately simulated the hydraulic head with a determination coefficient of 0.88. The calibrated model indicated that the change in storage is 0.56 m3/day indicating the study area constitutes highly productive zone and is recommended for groundwater developments.