The Aksu River, a quintessential inland river, exhibits elevated arsenic (As) concentrations in certain sections of its natural waters. Further investigation is necessary to determine the role of surface water and groundwater (SW-GW) exchanges in contributing to these high As concentrations. Both surface water and groundwater constitute crucial components of the basin water cycle, and the interaction between the two has been a central focus in basin water cycle research. In this study, a total of 59 groundwater samples and 41 surface water samples were collected along the river’s course within the basin. Among the groundwater samples, 18.64% exceeded the permissible drinking limit for As concentrations (10 μg/L), while 39.02% of the surface water samples exceeded this threshold. The water bodies in the Aksu River Basin are mildly alkaline, with total dissolved solids (TDSs) in surface water significantly surpassing those in groundwater. The chemical compositions of surface water and groundwater are strikingly similar, with the predominant anions being chloride (Cl−) and sulfate (SO42−) and the principal cations being sodium (Na+). The dissolution of silicate and carbonate minerals primarily influences the water chemistry characteristics of surface water and groundwater in the Aksu River Basin, followed by the dissolution of salt rocks. Human activities also play a major role in affecting the river’s water quality. The distribution of groundwater with elevated As content is entirely encompassed within the spatial distribution of surface water. Groundwater–surface water exchange plays a vital role in As enrichment in surface water.