The data on the heavy metal content at different soil depths derived from a multi-purpose regional geochemical survey in the Pearl River Delta (PRD) were analyzed using ArcGIS 10.0. By comparing their spatial distributions and areas, the sources of heavy metals (Cd, Hg, As and Pb) were quantitatively identified and explored. Netted measuring points at 25 ×25 km were set over the entire PRD according to the geochemical maps. Based on the calculation data obtained from different soil depths, the concentrations of As and Cd in a large area of the PRD exceeded the National Second-class Standard. The spatial disparity of the geometric centers in the surface soil and deep soil showed that As in the surface soil mainly came from parent materials, while Cd had high consistency in different soil profiles because of deposition in the soil forming process. The migration of Cd also resulted in a considerable ecological risk to the Beijiang and Xijiang River watershed. The potential ecological risk index followed the order Cd ≥ Hg > Pb > As. According to the sources, the distribution trends and the characteristics of heavy metals in the soil from the perspective of the whole area, the Cd pollution should be repaired, especially in the upper reaches of the Xijiang and Beijiang watershed to prevent risk explosion while the pollution of Hg and Pb should be controlled in areas with intense human activity, and supervision during production should be strengthened to maintain the ecological balance of As.