Archaeological sites in Egypt used to stand in dry environments as the ancient architects planned. Several sites are found nowadays bathed in water and seriously threatened by groundwater rise. Groundwater level rising became a phenomenon causing problems to temple construction. Abydos is one of these sites, located about 13 km west of the River Nile in El-Balyana District, Sohag Governorate. Abydos is thought to have been an important building for the Ancient Egyptians of kings of Dynasty I and II. In addition to the rising water level within this site, the increase of water salinity, due to evaporation, threatens and damages fragile carvings and paintings within the building. The main objective of this study is to monitor the groundwater rise and investigate its possible sources to protect this 4000 years old archaeological artifact against groundwater rising-related threats. Several field investigations and laboratory analyses were held including: Weekly surface water and groundwater levels monitoring, physical, chemical, biological, and isotope analysis of groundwater samples from the site. Water table measurements have been done in Abydos and the River Nile for two years. The analysis of the obtained data denoted that the main recharge source of Abydos which is a part of Quaternary aquifer is the recent River Nile water that comes from the Nile at Nag Hammadi to the south of the site. Water level at Nag Hammadi was recorded at 65.55 m asl, while in Abydos was about 63.68 m. Groundwater monitoring and chemical analyses revealed a dynamic flow regime under the given site. The flow regime is controlled by interaction between surface water of the River Nile and groundwater that is dependent on bedrock hydraulic features. The measured fluctuations in water levels in the River Nile have a significant correlation with the different groundwater flow dynamics found throughout the site with lag time about 6 to 7 days. Chemically, the water in Abydos area has different characteristics compared to that of the River Nile. An increase in Na+K – Cl due to mixing and water-rock interaction was observed. Bacteriological analysis indicated an increase in total coliform which might be originated from waste water.