Bioretention systems prove effective in purifying common persistent organic pollutants (POPs) found in urban rainfall runoff. However, the response process of the microecosystem in the media becomes unclear when POPs accumulate in bioretention systems. In this study, we constructed bioretention systems and conducted simulated rainfall tests to elucidate the evolution of micro-ecosystems within the media under typical POPs pollution. The results showed all POPs in runoff were effectively removed by surface adsorption in different media, with load reduction rates of >85 % for PCBs and OCPs and > 80 % for PAHs. Bioretention soil media (BSM) + water treatment residuals (WTR) media exhibited greater stability in response to POPs contamination compared to BSM and pure soil (PS) media. POPs contamination significantly impacted the microecology of the media, reducing the number of microbial species by >52.6 % and reducing diversity by >27.6 % at the peak of their accumulation. Enzyme activities were significantly inhibited, with reductions ranging from 44.42 % to 60.33 %. Meanwhile, in terms of ecological functions, the metabolism of exogenous carbon sources significantly increased (p < 0.05), while nitrogen and sulfur cycling processes were suppressed. Microbial diversity and enzyme activities showed some recovery during the dissipation of POPs but did not reach the level observed before the experiment. Dominant bacterial species and abundance changed significantly during the experiment. Proteobacteria were suppressed, but remained the dominant phylum (all relative abundances >41 %). Bacteroidota, Firmicutes, and Actinobacteria adapted well to the contamination. Pseudomonas, a typical POPs-degrading bacterium, displayed a positive correlation between its relative abundance and POPs levels (mean > 10 %). Additionally, POPs and media properties, including TN and pH, are crucial factors that collectively shape the microbial community. This study provides new insights into the impacts of POPs contamination on the microbial community of the media, which can improve media design and operation efficiency.