Although anthropogenic contamination has been regarded as the most important source of potentially toxic elements (PTEs) in soils of large river delta plains, the extent to which human activities affect PTEs in soils is worth exploring. This study used high density geochemical data to distinguish source patterns of PTEs in soils of the Pearl River Delta Economic Zone, a large industrialized and urbanized area in China. Enrichment factor, discriminant analysis, principal components analysis, cumulative distribution function, and positive matrix factorization were used to identify sources of PTEs in soils. The results indicated that parent material was the most significant factor affecting geochemical characteristics of PTEs in soils. Median concentrations of Cd, Cr, Cu, Hg, Pb, and Zn were 0.400, 88.5, 40.5, 0.143, 43.0, and 116.0 mg/kg for stream sediments, 0.333, 75.7, 39.0, 0.121, 42.6, and 98.5 mg/kg for deep soils, and 0.365, 74.0, 45.1, 0.143, 44.6, and 119.5 mg/kg for surface soils, respectively, all of which exceed relevant reference standards. Compared with stream sediments and deep soils, surface soils exhibit substantial concentrations of PTEs. Chemical weathering and erosion of parent materials distributed in the Pearl River Delta were the main sources of PTEs in soils. Diffuse contamination and many small local contamination sources distributed throughout the study area were the most significant anthropogenic sources of PTEs in surface soils. Intensive human activities failed to change the soil geochemical characteristics derived from the parent material at the regional scale. However, it could induce non-point source pollution and local severe PTEs pollution in surface soils.