Desert lakes have substantial impact on ecological and environmental changes in arid and semiarid zones. In this study, we chose the northern lake complex of a typical desert in northern China (Kubuqi Desert) as the study area, based on the test results of lake water, river water and groundwater samples of different burial depths in July-September 2024, combined with the analysis of the mineral characterization of the regional sediments, we comprehensively utilized the methods of mathematical statistics, Piper trilinear diagrams, Gibbs diagram, and ionic scaling relations to investigate the hydrochemical characterization and formation mechanism of the northern Kubuqi Desert lakes. The results showed that the lake water in the northern region of the Kubuqi Desert is weakly to strongly alkaline, and that the water chemistry of the lakes is dominated by the HCO3Na type, and lake complexes are early-middle stages of lake evolution. Evaporation and water-rock processes promote the transport of various ions in the lake complex, and positive cation exchange is dominant in the lakes of the northern Kubuqi Desert. The ionic ratio characteristics indicate that groundwater rock salt dissolution recharges the lake complex and that groundwater is the main source of recharge to the lakes in the northern part of the Kubuqi Desert rather than the Yellow River, and is dominated by shallow groundwater. The results of the study can help to reveal the hydrological significance of lakes in dry areas, as well as provide lessons and references for the ecological protection and restoration of lakes and wetlands in dry areas.