The present study integrates groundwater hydrochemistry to assess groundwater quality under expanding agricultural activities in Kharga Oasis, Egypt using field data, GIS technique and the multivariate statistical analysis (Factor analysis). A total of 144 groundwater samples were collected and analyzed for major ions and trace elements and the spatial distribution of physicochemical parameters was visualized with GIS. The result has been used to evaluate the groundwater quality in the area for drinking and irrigation purposes comparing with the World Health Organization WHO and Egyptian water standards (EHCW). Results revealed that 93.8% of the groundwater samples are freshwater with TDS  <  1000 mg/l, whereas the rest 6.2% are slightly saline (TDS 1000–3000 mg/l). 35.4% of the groundwater samples are unsuitable for domestic purposes due to the high level of hardness. The calculated water quality index WQI indicates that 88.2% of the samples are excellent for drinking use. Salinity hazard, sodium percent (Na %), sodium adsorption ratio (SAR), residual sodium carbonate (RSC), magnesium hazard (MH), Kelly’s ratio (KR), and soluble sodium percentage (SSP) were calculated to evaluate groundwater quality for irrigation purposes. According to the SSP values, 46% of the samples are good quality water for irrigation purpose, 71% of the samples are good to permissible for irrigation based on Na%, 79.2% of the samples are good for irrigation based on PI values and 91.1% of the samples are suitable for irrigation based on MH values. Based on the above results, most of the collected samples in the Kharga Oasis are unsuitable for drinking and agriculture under ordinary conditions without treatment while it is suitable for many industrial purposes. The factor analysis produced three factors which described 83.13% of the total variance. The results show that the concentrations of pH and HCO3− do not contribute to other chemical parameters. This study demonstrated that the hydrochemical analysis and GIS with statistical factor loading could deliver an influential tool to distinguish factors controlling the groundwater quality in Kharga Oasis area.