During a 12-month study period, the levels, distributions, sources and ecological risk of 16 polycyclic aromatic hydrocarbons (PAHs) were investigated in subsurface water of Shenyang (the largest urban industrial relocation base in China). The results showed that ΣPAH concentration ranged from 0.21 to 1.07 µg/L, in descending order as follows, summer, autumn, spring and winter. Comparing with the situations before relocation, there was a significant decrease in Fluorene, Phenanthrene and Anthracene levels. The content of Banzo[a]pyrene was in high level. Relatively high 16 EPA-PAHs concentrations were observed at downstream sites suggesting that after the industrial relocation, residual 16 EPA-PAHs in soil and sediments could be desorbed and resuspended in water. From a global perspective, contamination of subsurface water PAHs can be categorized as moderate level. Source analysis suggested that without industrial waste input, pyrogenic soureces were the major contributors for PAHs pollution in winter. Petrogenic and pyrogenic inputs were equally important sources for PAHs pollution in other seasons. Due to incomplete combustion of wood and coal, ecological risk of Banzo[a]pyrene was high in the winter, indicating that to alleviate 16 EPA-PAH contamination, segmented remediation and energy structure adjustment would be equally important in urban industrial relocation areas.