Lacustrine groundwater discharge (LGD) plays an important role in water resources management. Previous studies have focused on LGD process in a single lake, but the differences in LGD process within the same region have not been thoroughly investigated. In this study, multiple tracers (hydrochemistry, δD, δ18O and 222Rn) were used to compare mechanisms of LGD in Daihai and Ulansuhai Lake in Inner Mongolia, Northwest China. The hydrochemical types showed a trend from groundwater to lake water, indicating a hydraulic connection between them. In addition, the δD and δ18O values of sediment pore water were between the groundwater and lake water, indicating the LGD processes. The radon mass balance model was used to estimate the average groundwater discharge rates of Daihai and Ulansuhai Lake, which were 2.79 mm/day and 3.02 mm/day, respectively. The total nitrogen (TN), total phosphorus (TP), and fluoride inputs associated with LGD in Daihai Lake accounted for 97.52 %, 96.59 %, and 95.84 % of the total inputs, respectively. In contrast, TN, TP and fluoride inputs in Ulansuhai Lake were 53.56 %, 40.98 %, and 36.25 %, respectively. This indicates that the pollutant inputs associated with LGD posed a potential threat to the ecological stability of Daihai and Ulansuhai Lake. By comparison, the differences of LGD process and associated pollutant flux were controlled by hydrogeological conditions, lakebed permeability and human activities. This study provides a reference for water resources management in Daihai and Ulansuhai Lake basins while improving the understanding of LGD in the Yellow River basin.