Three dimensional lithologic modeling techniques have been used for detailed characterization and groundwater flow modeling of the Quaternary aquifer system of the Sohag area, Egypt. Well log data were used for building the lithologic model using RockWorks. A groundwater flow model, facilitated by MODFLOW 2000, was built using results of the lithologic model. The obtained lithologic model honored the well log data and revealed a complex sedimentary system, which is mainly composed of six lithologic categories: clay, clay and sand, fine sand, coarse sand, sand and gravel, and gravel. Inter-fingering and presence of lenses are the main characteristics of the sedimentary basin in the study area. A wide range of hydraulic conductivities is present, which vary spatially and control the groundwater flow. Heterogeneity of the aquifer system is spatially represented where different hydraulic conductivities are found in the different directions. Sandy layers tend to be connected. Hydraulic continuity is represented by inter-fingering and connection of sandy materials within the aquifer system.