Bioretention facilities have proven highly effective in removing pollutants from runoff. However, there is a concerning paucity of research on the contamination characteristics and associated risks posed by refractory pollutants in these facilities following long-term operation. This research focuses on the distribution, sources, microbial community impact, and human health risks of pollutants in eight bioretention facilities that have been operational for 5–11 years. The results showed that the distribution of Cu, Zn, and Cd was closely related to anti-seepage measures. PAHs, PCBs, and OCPs primarily accumulated in the surface, with concentrations ranging from 7.42 to 20.34 mg/kg, 31.8–77.3 μg/kg, and 60.5–163.6 μg/kg, respectively. Their concentrations inversely correlate with the depth of the media. Although the majority of contaminants remained below their respective risk thresholds, their concentrations typically exceeded those of background soil values, indicating an enrichment phenomenon. Source analysis revealed that PAHs primarily originate from oil combustion, PCBs were linked to their related industrial products, DDTs had their main sources in technical DDx and residues from the use of dicofol, while HCHs were traced back to historical residues from agricultural activities. Microbial α-diversity (Chao 1 and Shannon) decreased by 8.3–23.4% and 0.8–4.4%, respectively, in different facilities after long-term operation. The most dominant microbial phylum in the facilities was Proteobacteria (all relative abundances >48%). The total relative abundance of dominant genera was 6.7–34.3% higher than the control site, and Pseudomonas, a typical POPs-heavy metal degrading bacterium, had the highest relative abundance (>1.2%). Cu, Zn, and Cd present no non-carcinogenic risks and have low potential ecological risks. However, the lifetime cancer risk for PAHs is 10−6 ∼10−4 in most facilities and is of concern. The cancer risk for PCBs is acceptable, while OCPs pose a low cancer risk only for children.
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