The consumption of water and food crops contaminated with metals is a major food chain route for human exposure. We investigated the health risks of metals in Yellow River (YR) water, farmland soil and spring wheat in the Baotou region, northern China. Data indicated that long-term irrigation with polluted YR water led to metal accumulation in local farmland soil and spring wheat. The consumption of YR water and spring wheat in Baotou region can cause adverse health effects to local people, specifically because of Hg, Pb, and Se in YR water and Cu, Zn, Cd, and Mn in spring wheat. The integrative risk of various metals depends mainly on the spring wheat intake. Current results emphasized the need for routine monitoring and management in order to avoid contamination of YR water and spring wheat from the wastewater irrigation system in Baotou region.