The study of pollution and risk assessment of surface water in watersheds is important for the use and management of surface water, as well as for the stability of ecosystems and human health. This study focused on a typical watershed in an arid zone, the Urumqi River basin; divided the basin into upper, middle, and lower reaches according to the main uses of the surface water in the region; and collected surface water samples from the basin. We collected 41 surface water samples from the upper, middle, and lower reaches of the Urumqi River Basin, a typical arid zone watershed. The characteristics and spatial distribution of metal elements in the surface waters of the basin were analysed, the pollution status was evaluated, and risk assessments of the effects of these metal elements on natural ecosystems and human health were carried out. The results showed that (1) the average concentration of the metal element Al in the surface water of the Urumqi River Basin was 663.73 µg·L−1, which was 3.3 times that of the standard limit value (200 µg·L−1), with an exceedance rate of 100%, and the standard deviation value was 136.05 µg·L−1, with a large difference in spatial distribution. Spatial distributions for Al, Cu, Cr, Fe, Mn, and Zn were higher upriver and midstream than downriver, and for Pb and As, they were higher upriver, midstream, and downriver than downriver. (2) The values of the single-factor pollution index of the metal elements Zn, As, Pb, Mn, Cr, and Cu in the upper, middle, and lower reaches of the watershed were all less than 1, which is within the safe range. The integrated pollution indexes of 0.03~0.27 were all less than 0.7, which is within the safe range, and the integrated pollution of the upper reaches was significantly greater than that of the middle and lower reaches. (3) The total ecological risk of the basin ranged from 0.09 to 13.72, which is much lower than the low-risk indicator value of 150, and the ecological risk of the upper reaches was higher than that of the middle and lower reaches. (4) The health risk assessment showed that the total health risks of the eight metal elements to adults and children showed an upstream > downstream > midstream pattern, all of which exceeded the ICRP recommended value (10−5). The average annual total health risks of the carcinogenic metal elements chromium and arsenic to adults and children were 10−6 and 10−5 a−1, respectively, with arsenic concentrations exceeding the ICRP recommended value (10−5). Arsenic and lead in the surface waters of the Urumqi River Basin are important indicators of health risk and need to be prioritised as indicators for environmental risk management.
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