The main water resources for Egypt are the River of the Nile and groundwater. Evaluating and assessing these vital resources is crucial for liable usage and meeting the growing demand for water. In Assiut area, groundwater stands as the second most significant freshwater source, serving all sectors including industrial sector, agricultural sector, and lastly domestic sector. Unfortunately, the groundwater in Assiut governorate face the imminent threat of contamination, primarily due to agricultural and other activities. A hydrochemical investigation was conducted graphically and spatially within GIS environment in the limestone Eocene aquifer of the designated study area. This research involved the collection and analysis of twelve groundwater samples to realize the physiochemical characteristics, providing insights into the hydrochemistry of the water. The assessment of water quality involved evaluating 16 parameter and comparing them to drinking water and irrigation standards set by both the Organization of World Health (WHO) and the Egyptian Specifications (ES). In this study 8 main parameters are selected due to their importance which are; Electrical Conductivity (EC), pH, Total Dissolved Solids (TDS), Nitrate (NO3-) and Fluoride (F-). The analysis indicates that the groundwater is not entirely suitable for drinking, particularly concerning TDS, Chemical Oxygen Demand (COD), and Total Organic Carbon (TOC). In certain samples, the parameters concentrations surpass the allowable limits defined by both WHO and ES. This is due to the increase in domestic and industrial wastewater discharge the stretch, as well as other harmful anthropogenic activities, and human interventions. GIS-based spatial analysis successfully identified vulnerable areas where groundwater contamination is most severe. Elevated levels of TDS, COD, and TOC were found in several locations, posing risks for domestic use and irrigation. The Piper diagram analysis indicated that the predominant water type is calcium-chloride-bicarbonate, suggesting groundwater is influenced by precipitation and water–rock interactions with carbonate rocks. The Water Quality Index (WQI) analysis was applied, showing that the northern part near the New Assiut Barrage (samples 10 and 11) exhibits a high degree of contamination, making the water unsuitable for drinking according to WHO and Egyptian standards. The findings of this study could help the policymakers to take the suitable action to protect people and animals’ health form contaminated water.