In order to evaluate the quantitative relationship between salinity and fluoride concentration and their control factors in Lake Ulungur in Xinjiang, China, this study develops a model for predicting stable state and dynamic water salinity based on water mass balance and solute balance. The input parameters are rainfall, evaporation, river recharge, groundwater recharge, groundwater outflow, and their associated salinity. The concentration of fluoride can also be modeled following the same approach, which provides another constraint on input parameters. The results show that the groundwater outflow significantly affects the salinity and fluoride concentration in lake water, with increasing outflow leading to lower salinity and fluoride concentration in Lake Ulungur. The rise of lake water level leads to increased outflow of groundwater in Lake Ulungur between 2010 and 2020, and the salinity and fluoride concentration in lake water decreased slowly. Our model predicts that the salinity of the Lake Ulungur in the new stable state is 1.68 g/L, and the concentration of fluoride is 1.70 mg/L, but it will take roughly 50 years to reach the new stable state given that the outflow rate remains constant.