The headwater region of inland China is immensely important for sustaining livelihoods and maintaining ecological balance, highlighting the need to characterize and assess water quality in this region. The aim of this study is to acquire a comprehensive understanding of the spatiotemporal variation characteristics of river water chemistry and to identify the sources of major ions in the Binggou River Basin, Northwest China. The results show that the water of the Binggou River is neutral freshwater. SO42− is the major anion, Ca2+ is the major cation and the river type is Ca–Na–SO4–HCO3. The concentrations of Na+, Mg2+, SO42−, NO3−, and total dissolved solid are slightly higher than the global average. The seasonal variations of major ion concentrations in the river are highest in winter but lowest in autumn, whereas the spatial variations are greater in the east branch than in the west branch and upstream compared with downstream. Source analysis of the ions indicates that rock weathering is the main source of ions, followed by human activities such as farmland fertilization and coal burning. Water quality analysis shows that the river water is suitable for drinking and irrigation, but the water quality is relatively poor in areas with more human activity, which indicates that human activity greatly influences water quality.