Based on water sampling of the upper reaches of the Syr River and its tributaries from the parts of Aral Sea Basin in Kyrgyzstan, the chemical compositions of river waters were systematically analyzed for revealing the hydrochemical characteristics and evaluating the water quality. Research indicates that there are some differences in ion concentration between the low-flow season (LFS) and high-flow season (HFS), but the hydrochemical classification reflected that all water samples fall in the calcium bicarbonate category, except that only three samples fall in the not dominant category during the LFS. The water quality classification shows that the water samples fall in the excellent to good categories for irrigation use. The analysis shows that the main ions of river waters come from the weathering of rocks, and the dissolution of carbonates is higher than that of silicates. Human activities have had an impact on the waterbody, especially inferred from the indicators of NH4-N and fecal coliform (FC). FC groups were detected in some rivers, in which the detection rate at the high-water level increased. The contents of potentially toxic elements are lower than international drinking water standards, but there are clustering differences between the LFS and HFS. There may be anthropogenic intrusions of Cu, Pb, and Zn during the LFS period and of Cu, Pb, Zn, and Cd during the HFS period. The results fill the gaps in the study of the hydrochemical composition and water quality assessment in the Aral Sea Basin and will also provide a basis for water resource management and for the study of water quality evolution in the future.