The spatio-temporal variation and temporal changes in the sources of Cr, Pb, Cd, Hg, and As in soil on the Hangzhou-Jiaxing-Huzhou (H-J-H) Plain were analysed based on 4,359 soil samples collected in 2002 and 2012. Geostatistical and spatial analysis methods were used to explore the spatio-temporal variation in the pollution levels and 'pollution hotspots' for potentially toxic elements (PTEs), and the positive matrix factor model was used to quantitatively appoint and analyse temporal changes in PTE sources. The results indicated that the PTE content in most parts of the survey area were at a safe level in both 2002 and 2012, but a clearly upward trend was detected for Cr, Pb, and Cd. Moreover the pollution index for Cr, Pb, Cd, and the Nemerow composite pollution index increased in the west but decreased in the east of the H-J-H Plain from 2002 to 2012. The pollution index for Hg and As presented the opposite spatial pattern. It is obvious that there have been changes in the spatial pattern of pollution hotspots for PTEs on the H-J-H Plain from 2002 to 2012. Four sources of PTEs in soil were quantitatively appointed. In 2002, 2012, the dominant sources of Cr, Cd, Hg, and As were soil parent materials, industrial activities, atmospheric deposition and agricultural inputs, respectively. The dominant source of Pb in the soil changed from traffic emissions to soil parent materials, indicating the benefit of banning the use of leaded gasoline in China. This study highlights the importance of monitoring soil environmental quality and highlights the significance of spatio-temporal variation in PTEs in suburban zones or transitional areas undergoing rapid industrialization and urbanization, like the H-J-H Plain.