Samples of river water and groundwater from Quaternary (QA), sandstone (SA), Taiyuan formation (TA), and Ordovician limestone (OA) aquifers in the Suxian coal-mining district, Anhui Province, China were collected. Their physicochemical properties, and major ion and isotopic compositions were determined. The samples were alkaline, with pH values exceeding 8, and the total dissolved solids concentrations depended on the water source. The δD and δ18O contents were highest in the river water samples and lowest in the SA groundwater. The isotopic characteristics of the QA and OA groundwaters suggest recharge by rainfall and surface water. The isotopic characteristics of river water were controlled mainly by evaporation. Water–rock interactions, the flow rate, and the main water sources were the most important influences on groundwaters in QA, OA, and TA, but the properties of SA groundwater were controlled by static reserves. Two discriminant functions, explaining more than 98.2% of the total variances, indicated that QA, TA, and OA were hydraulically connected. Three groundwater sources were identified as end-members, and a conceptual model was established to calculate water mixing ratios.