Studying groundwater flow systems is important for water resources management, for pollution prevention and for maintaining the ecological balance in arid and semi-arid areas. Systematic geophysics and hydrogeological investigations allow us to define the thickness of the Quaternary sedimentary layer, the lateral boundary of the groundwater system, and the depth and basement of water circulation. Hydrogeochemistry and environmental isotopes are used to gain insights into the recharge process, water-rock interactions, hydraulic characteristics and groundwater retention time and to identify groundwater flow systems at all levels in the Aksu River Basin. Owing to the dissolution of carbonate and gypsum minerals and evaporites, cation exchange between Ca 2+ (Mg 2+) and Na + (K +), and the evaporation-concentration effect, concentrations of specific ions (SO 4 2-, Cl -, Na +) and [total dissolved solids](javascript:;) (TDS) gradually increase along the flow direction and decrease with depth (indicating that they belong to different groundwater flow systems (GFSs)). Furthermore, interpretation of stable isotope concentrations such as δ 18O values suggests different degrees of depletion in the horizontal and vertical directions. Combined with the unique structural framework (namely the Wensu uplift, Wushi sag, and Awat sag), the particle size variation of loose sediments and the distribution and aggregation of phreatic water with high F and As and soil salinization show the existence of the surface-ground water interaction and the distribution pattern of multiple local GFSs. The vertical zonation of 3H and 14C isotope concentrations and estimates of groundwater [residence](javascript:;) time (modern to 24000 years) further illustrate the hydrodynamic cycle of the local and regional GFSs. The hydrodynamic and hydrochemical characteristics confirmed the distribution of GFSs and the complex mixing relationships between GFSs in the Aksu River Basin under the tectonic conditions since the Neogene in the South Tianshan Mountains.

In arid and semi-arid areas, groundwater flow is a potent geological agent. The typical profile of Aksu river basin was chosen as the research object. First, the survey region’s geological background and hydrological conditions were systematically analysed. Combined with geophysical and remote sensing characteristics, the thickness change of the Quaternary loose layer, boundary of the subaqueous system, and basement of the water circulation depth were revealed. Hydrogeochemistry and environmental isotopes were applied to explain the recharge-runoff-discharge process, water-rock interaction, movement law, and residence time of surface-groundwater. Owing to the dissolution of carbonate and gypsum minerals and evaporates, cation exchange between Ca 2+ (Mg 2+) and Na + (K +), and the evaporation-concentration effect, specific ions (SO 4 2-, Cl -, Na +) and [total dissolved solids](javascript:;)(TDS) from the surface to groundwater gradually increased with the flow direction and gradually decreased with depth. This difference was more evident in the downstream discharge area, which indicated that they belonged to different groundwater flow systems(GFSs).Because of the elevation effect of the recharge source, the δ 18O values in different sections showed different degrees of depletion in the horizontal and vertical directions. In [association with](javascript:;) the structural ‘one convex and two concaves’ frameworks and the particle size variation of loose sediments, it reflected the distribution pattern of multiple local GFSs. The vertical zonation between the 3H and 14C isotope concentrations and the recorded groundwater [residence](javascript:;) time (modern-24000years) further illustrated the existence of intermediate and regional GFSs. Three surface-conversion boundary key zone (GFS cbz) were identified, and the GFS conceptual model was established. Finally, the corresponding relationship between the GFSs and the environmental effects, such as the distribution and aggregation of phreatic water with high F and As and soil salinization, were analysed, which had important theoretical significance for protecting the ecological balance of Aksu River basin.