Abydos is one of the oldest archaeological sites in Upper Egypt. It is located in western flood plain of the River Nile at Sohag Governorate, and about 13 km west of the River Nile course. However, this site is threatened by groundwater rise. For any archaeological site, it is necessary to be placed within its wider natural environment, and to thoroughly understand the natural hydrogeological balance and possible changes that are being forced upon it by nature or human activities. It is demonstrated that groundwater and soil-moisture monitoring, combined with 3D transient modeling are potentially effective routines to improve the understanding of preservation conditions in complex archaeological surroundings and, therefore, protection of archaeological constructions in situ. Ultimately, the numerical model can then be used as a tool to predict changes in hydraulic head and phreatic levels as a consequence of natural or human changes forced upon it. Therefore, a 3D-grondwater flow modeling approach was presumed to model the groundwater level changes within Abydos area and to investigate its possible recharge so as to suggest the most feasible protection solutions for this archaeological site by suggesting appropriate scenarios. The finite element model code FEFLOW was used to simulate groundwater flow at Abydos site. Based on borehole descriptions, geological mapping, hydrogeological data, and field observations, a numerical model was constructed using 2 model layers. The model layers were constructed using a digital elevation model, spatially interpreted borehole data and cross sections. The model was run first under early conceptual or intermediate (steady state) modeling stages, which provided valuable information and understanding of the hydrological system facilitating improvement of the monitoring, program. The model was calibrated against field observations. The transient numerical modeling and simulated groundwater pathlines indicated that groundwater recharge is mainly from southeast.