There is a growing public concern over the potential accumulation of heavy metals in agricultural soils in China owing to rapid urban and industrial development and increasing reliance on agrochemicals in the last several decades. Excessive accumulation of heavy metals in agricultural soils may not only result in environmental contamination, but elevated heavy metal uptake by crops may also affect food quality and safety. The present study is aimed at studying heavy metal concentrations of crop, paddy and natural soils in the Pearl River Delta, one of the most developed regions in China. In addition, some selected soil samples were analyzed for chemical partitioning of Co, Cu, Pb and Zn. The Pb isotopic composition of the extracted solutions was also determined. The analytical results indicated that the crop, paddy and natural soils in many sampling sites were enriched with Cd and Pb. Furthermore, heavy metal enrichment was most significant in the crop soils, which might be attributed to the use of agrochemicals. Flooding of the paddy soils and subsequent dissolution of Mn oxides may cause the loss of Cd and Co through leaching and percolation, resulting in low Cd and Co concentrations of the paddy soils. The chemical partitioning patterns of Pb, Zn and Cu indicated that Pb was largely associated with the Fe-Mn oxide and residual fractions, while Zn was predominantly found in the residual phase. A significant percent fraction of Cu was bound in the organic/sulphide and residual phases. Based on the 206Pb/207Pb ratios of the five fractions, it was evident that some of the soils were enriched with anthropogenic Pb, such as industrial and automobile Pb. The strong associations between anthropogenic Pb and the Fe-Mn oxide and organic/sulphide phases suggested that anthropogenic Pb was relatively stable after deposition in soils.