The characteristics and sources of the hydrochemical composition of natural water are mainly influenced and limited at the basin scale by what factors, this has become a focal issue of environmental change in the middle latitude areas and even globally. In this study, three large drainage systems (Junggar, Yili, and Erlqis) in the north of the Tianshan Mountains were selected to study the hydrochemistry of different river basins and understand the relevant causes and attributions of different water bodies in arid environments in the Central Asian Orogenic Belt (CAOB). Natural water samples from the three drainage systems and their hydrochemical data, combined with literature data of the north and south Tianshan Mountains and surrounding areas, were systematically collected and comprehensively compared with other higher, middle, and low latitude watersheds with different climate conditions. The results show that the total dissolved solid concentrations in the CAOB drainage systems are generally higher than those of rivers in Chinese monsoon and humid regions, and also higher than the world average level. The relative concentrations of different ions are similar to those of rivers in the monsoon region of eastern China and most rivers in the world dominated by carbonate weathering. The ionic compositions of surface water bodies from different sub-basins in the study area are distributed near the Ca apex in the piper diagram, while those of phreatic and confined groundwater samples tend to the Na apex. The compositional differences in the anions are not like those in the cations, rarely distinguishable for these different water types. In a sub-drainage basin scale from I to VIII sub-basins in the study area, major ion concentrations and distributions in these basins are evidently heterogeneous. Almost all the cation and anion concentrations span > 1 order of magnitude, especially sodium and chlorine; however, the calcium and alkalinity concentrations and distributions are relatively homogeneous for some basins in the Junggar and Yili drainage systems. The relative homogeneity between anions and the relative heterogeneity between cations can be recognized in the ion chemistry of natural water samples between different types, indicating that the composition and distribution of cations in water is more conducive than those of anions to identifying the differences and commonalities between different regions. Atmospheric precipitation plays a key role on the hydrogeochemical process in the north of the Tianshan Mountains, and the elevation differentiation of chemical weathering and ion concentrations are closely related to it. The positive correlation between total solute flux and runoff cannot be explained by the dilution effect, indicating that hydroclimatic factors such as runoff and aridity have a strong effect in limiting the hydrochemistry of natural water bodies in the study area.