Thoroughly investigating the evolution of groundwater circulation and its controlling mechanism in the Aksu River Basin, where human activities are intensifying and the groundwater environment is increasingly deteriorating, is highly urgent and important for promoting the theory, development and implementation of groundwater flow systems (GFSs) and protecting groundwater resources. Based on a detailed analysis of the sediment grain size distribution, chronology, electrofacies, glacial sedimentary sequence, palaeoclimate indicators and existing groundwater age, this paper systematically reconstructs the palaeosedimentary environment of the basin-scale aquifer system in the study area and scientifically reveals the evolutionary pattern and formation mechanism of the GFS. The results showed that the later period of the late Pleistocene experienced a rapid downcutting erosional event caused by tectonic uplift, and the sedimentary environment transitioned from a dry–cold deep downcutting environment in the Last Glacial Maximum (LGM) to a coarse-grained fast-filling fluvial facies sedimentary environment in the Last Glacial Deglaciation (LDP) as the temperature rose; then, it shifted to an environment of fine-grained stable alternating accumulation of fluvial facies and lacustrine facies that was dominated by the warm and arid conditions of the Holocene megathermal period (HMP); this process changed the previous river base level via erosion, glacier elongation or shortening and river level, thus resulting in a complex coupling relationship between the palaeosedimentary environment, palaeoclimate and basin GFS. Furthermore, the existing GFS pattern in the basin exhibits a vertically unconformable groundwater age distribution, which indicates that it is the outcome of the complex superposition of groundwater flow controlled by the palaeosedimentary environment in different periods. Therefore, neotectonic movement and climate fluctuation have jointly acted on the variation in the river level, resulting in the “seesaw” effect, thereby fundamentally controlling the strength of the driving force of groundwater and resulting in the gradual evolution of the GFS from the fully developed regional GFS pattern during the LGM to the current multihierarchy nested GFS pattern.

A numerical model was developed to investigate contaminant transport and the concentration-control performance of groundwater circulation wells (GCWs) in a heterogeneous porous-fractured aquifer beneath a landfill site. The effects of aquifer structure, injection-extraction rate, and well configuration on contaminant plume evolution and simulated concentration responses were evaluated. Results showed that aquifer heterogeneity controlled contaminant migration patterns. In fracture-free media, plume evolution was mainly governed by regional groundwater flow and advective-dispersive transport, whereas fractures promoted preferential transport, earlier breakthrough, and greater spatial variability in contaminant distributions. Increasing the injection-extraction rate enhanced circulation-induced hydraulic gradients and promoted mean concentration reduction under the simulated conditions, with a more pronounced response in fractured media. The single-borehole vertical circulation well provided less extensive plume-scale concentration control than the evaluated multi-well configurations. However, comparisons among configurations with different numbers of boreholes reflect the combined effects of well number, spatial arrangement, and individual well flow-rate distribution. The simulated concentration reductions resulted from groundwater extraction, prescribed clean-water injection, hydraulic flushing, and solute redistribution, rather than an equivalent percentage of contaminant mass removal or destruction. These findings indicate that concentration-control performance is jointly influenced by aquifer heterogeneity, preferential flow structures, and circulation-induced hydraulic conditions. They also provide a numerical basis for the preliminary evaluation of GCW configurations and operating scenarios, supporting more informed groundwater pollution-control planning and sustainable management of landfill-affected aquifers.