Groundwater plays an irreplaceable role in all aspects of the Loess Plateau. In this study, the loess phreatic water (LPW) and bedrock phreatic water (BPW) in the Ning County area (NCA) were sampled and analyzed, and the characteristics and controlling factors of groundwater were determined by using statistical analysis, hydrochemical methods, and hydrogeochemical simulation. The results indicated that the groundwater in the NCA was alkaline as a whole, and the average pH values of LPW and BPW were 8.1 and 7.8, respectively. The mean values of TDS concentrations of LPW and BPW were 314.9 mg/L and 675.3 mg/L, and the mean values of TH contents were 194.6 mg/L and 286.6 mg/L, respectively, which were mainly divided into hard fresh water. The Piper diagram illustrated that the hydrochemical type of groundwater in the NCA was mainly the HCO3·Ca type. The main recharge source of groundwater was atmospheric precipitation, and it was affected by evaporation to a certain extent. The linear relationships of δ18O and δ2H of LPW and BPW were δ2H = 6.998δ18O − 3.802 (R2 = 0.98) and δ2H = 6.283δ18O − 10.536 (R2 = 0.96), respectively. Hydrochemical analysis indicated that the groundwater in the NCA was mainly controlled by rock weathering and cation exchange. BPW was affected by the dissolution of gypsum. The possible mineral phases were identified on the basis of the main soluble minerals in the aquifer, and hydrogeochemical reverse simulations were performed. The dissolution of calcite, illite, and hornblende, and the precipitation of dolomite, plagioclase, and microcline occurred on both the LPW and BPW pathways.