Wastewater irrigation can increase metal concentrations in soil and wheat, thereby posing metal-associated health risk via food ingestion. We investigated levels of mercury (Hg) and arsenic (As) in roots, husks, stems, leaves, and grains of wheat and their fractionations in farmland soil from Baiyin City, an industrial and mining city, northwest China. Results show that the mean concentrations of Hg in soils from Dongdagou and Xidagou stream in Baiyin were 8.5 times and three times higher than local soil background values, respectively. Those of As were 4.5 times and 1.6 times higher, respectively. Most Hg and As were mainly accumulated in wheat leaves. The spatial distributions of As in soils and grains exhibit a very similar pattern, which suggest that As pollution in soils might be predicted by its level in wheat grains. Residual fractions for Hg (RES-Hg) and As (RES-As) are the highest compared to other fractions, indicating weak mobility of Hg and As in soil. The crop oral intake hazard quotients of both Hg and As for children were approximately two times higher than that for adults, indicating that children have higher exposure risks to Hg- and As-contaminated wheat. The crop oral intake was the main route of exposure causing non-carcinogenic and carcinogenic risk for local residents.