Hydrochemistry of groundwater is important in coal mines because it can be used for understanding water–rock interaction and inrush water source identification. In this study, major ion concentrations of groundwater samples from the loose layer aquifer (LA), coal-bearing aquifer (CA) and Taiyuan Formation limestone aquifer (TA) in the Qingdong coal mine, northern Anhui province, China, have been analyzed by a series of statistical methods for identifying the source of chemical constituents in groundwater and the source of inrush water. The results indicate that the mean concentration of the major ions in the LA were ordered as follows: HCO3− > SO42− > Na+ + K+ > Cl− > Ca2+ > Mg2+ > CO32−, whereas average values of the CA in decreasing order are SO42−, Na+ + K+, HCO3−, Cl−, Ca2+, Mg2+ and CO32−, and the major ion concentrations of the TA have the following order: SO42− > Na+ + K+ > Ca2+ > HCO3− > Cl− > Mg2+ > CO32−, and most of the samples are Na-SO4 and Ca-SO4 types. TDS content in water increases with aquifer depth, whereas the pH values ranged from 7.1 to 8.9, indicating a weak alkaline environment. Two sources (weathering of silicate minerals and dissolution of evaporate minerals) have been identified by principal component analysis responsible for the chemical variations of the groundwater, and their contribution ratios have been quantified by Unmix model. Moreover, based on the Q-mode cluster and discriminant analyses, the samples with known sources have been identified correctly to be 95.7% and 97.6%, respectively, and the samples with unknown sources have been determined with high probability (78–100%).