Water resources and water quality are restrictive factors in the Chinese Loess Plateau (CLP), a unique area with most severe soil erosion, fragile ecology and water shortage. River and well water samples were firstly analyzed, and multiple methods and indexes, including principal component analysis (PCA), correlation analysis (CA), sodium adsorption ratio (SAR), water quality index (WQI), hazard quotient (HQ), and hazard index (HI), were used to investigate characteristics, water quality and health risk assessment of trace elements in CLP. The average trace elements concentrations were higher than the world average with a slightly alkaline characteristic. PCA and CA showed that Al, Fe, Li, B, As, and F had natural origins from loess weathering and leaching; Cr, Pb, Cd, Cu, Ag, and Tl were mainly from anthropogenic input; Co, Ni, and Mn were dominated by both anthropogenic and natural sources. The poor river water quality was mainly related with high sodium (alkalinity) and salinity hazard. The poor well water quality samples with high WQI values, especially for As, Cr, and B, were distributed in the northwest and the Fenhe River sub-basin. The pollution level of trace elements in rivers in CLP was in medium level compared with other rivers worldwide. Arsenic pollution was the worst in well water and was the potential pollutant in river water especially for children. Arid climate together with anthropogenic input and special water characteristics (high Na, pH, and low Ca) aggravated As pollution. More work should be done to monitor the secular variation and remove As in the high As areas. The results of this study can provide the basic data for efficient water management and human health protection in CLP. Display omitted •The pollution level of trace elements in Loess Plateau is in medium level.•As, Cr and B were the main pollutants of the natural waters.•Arsenic was the most important pollutant for non-carcinogenic risks.•Poor quality waters are distributed in the northwest and Fenhe River basin.•Arid climate and anthropogenic input are the main reasons for water pollution.