Metallic ore mining causes heavy metal pollution worldwide. However, the fate of heavy metals in agrosystems with long-term contamination has been poorly studied. Dongchuan District (Yunnan, southwest China), located at the middle reaches of the Xiaojiang River, is a well-known 2000-year-old copper mining site. In this work, a survey on soil heavy metal contents was conducted using a handheld X-ray fluorescence instrument to understand the general contamination of heavy metals in the Xiaojiang River Basin. Furthermore, river water, soil, and rice samples at six sites along the fluvial/alluvial fans of the river were collected and analyzed to implement an environmental assessment and an evaluation of irrigated agrosystem. V, Zn, and Cu soil levels (1724, 1047, and 696 mg·kg−1, respectively) far exceeded background levels. The geo-accumulation indexes (Igeo) showed that cultivated soils near the mining sites were polluted by Cd and Cu, followed by Zn, V, Pb, Cr, Ni, and U. The pollution index (Pi) indicated that rice in the area was heavily polluted with Pb, Cr, Cd, Ni, Zn, and Cu. The difference in orders of metal concentrations between the soil and rice heavy metal contamination was related to the proportion of bioavailable heavy metals in the soil. The crop consumption risk assessment showed that the hazard quotient exceeded the safe threshold, indicating a potential carcinogenic risk to consumers. The Nemerow integrated pollution index and health index indicated that the middle of the river (near the mining area) was the heaviest polluted site.
