In this study, the natural Cu background concentration and Cu natural and anthropogenic contamination in soil, water and crop were investigated systematically in Huangshi area. The results show that regional geology is the dominant factor controlling the natural Cu background concentration in soil and water, and that pH is important to control the vertical distribution of Cu in soil under the same geographical and climatic conditions. The mineralization of rock bodies causes the natural Cu increase in soil and water, whereas, a large number of mining-smelting plants and chemical works are the main sources of Cu anthropogenic contamination. Cu in naturally and anthropogenically polluted soil displays differences in total and available contents, vertical distribution patterns and physico-chemical properties, the same happens in water.