The concentration level related to toxicities of trace elements in drinking water, rice, wheat flour, and their associated negative impacts on human health have become an emergent issue in China. Because Xinjiang is the largest province in China with the majority of arable pasture land available for cultivation, it is important to analyze the concentrations of trace elements in relation to their toxicities in water, rice, and wheat flour and to investigate the health risk differences between agricultural and pastoral areas in Bay County, Xinjiang. The study results showed that (1) metal concentrations from drinking water, rice, and wheat flour were within the permissible limits; (2) concentration levels of trace elements and their total risk from drinking water and rice were higher in the agricultural areas than those in the pastoral areas, whereas concentration levels of trace elements and their total risk from wheat flour were higher in the pastoral areas than those in the agricultural areas; (3) the concentration level of the trace elements in rice were higher than in the wheat flour, but the risk from the wheat flour was higher than the risk from rice; (4) total non-cancer risk from the flour (HIf) in both areas exceeded the respective safe reference doses; (5) total cancer risk from the wheat flour, rice, and water exceeded the safety limit (1 × 10−4); (6) for the exposed population, arsenic was suggested as the most evident pollutant leading to carcinogenic concerns regarding the water, rice, and wheat flour; (7) the risk index from the wheat flour made up the highest percentage both in the total cancer risk and the non-cancer risk, followed by rice and then water; and (8) the human health risk was attributed to influence from the local environment in the agriculture areas, while it was attributed to the external environment in the pastoral areas.

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