The shortage in surface water quantities led to a shift in dependence on the groundwater as an alternative water source in southern parts of Iraq. The groundwater is decreasing in quantity and water quality is degrading due to different factors. Therefore, it is important to assess the groundwater quality of the Missan Governorate of the country by analyzing the physicochemical parameters and distinguishing the probable sources of contaminants in the area. The present study used water quality diagrams and statistical methods such as factor analysis and agglomerative cluster analysis to determine the sources of chemical ions in the forty-four groundwater samples collected from wells in the study area. In addition, the Water Quality Index (WQI) was calculated to evaluate the groundwater quality by combining the parameters into a single index. The WQI results varied from − 66.27 to 1064.13 indicating that the groundwater is unsuitable for drinking at various places and good in quality at most of the wells of the area. The main factors that contribute to the differences in the groundwater quality include the variation in geological materials, influence of climate such as the high rate of evaporation, and anthropogenic factors such as industrial activities in central areas such as oil production in the Bazergan oil field. The most affected wells by the petroleum industry that were clustering in cluster R1which show high levels in most water chemistries. The results have implications for the management of the groundwater resources, which are expected to be under more risk of contamination in near future.