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In this study, nine congeners of polybrominated diphenyl ethers (PBDEs) and sixteen congeners of polycyclic aromatic hydrocarbons (PAHs) were measured in water samples to elucidate their spatial distribution, congener profiles, sources and ecological risks in the Guanlan River during both the dry season (DS) and the wet season (WS). The concentration of Σ 9 PBDE ranged from 58.40 to 186.35 ng/L with an average of 115.72 ng/L in the DS, and from 8.20 to 37.80 ng/L with an average of 22.15 ng/L in the WS. Meanwhile, the concentration of Σ 16 PAHs was ranged from 121.80 to 8371.70 ng/L with an average of 3271.18 ng/L in the DS and from 1.85 to 7124.25 ng/L with an average of 908.11 ng/L in the WS. The concentrations of PBDEs and PAHs in the DS were significantly higher than those in the WS, probably due to the dilution of the river during the rainy season. Moreover, the spatial distribution of pollutants revealed decreasing trend in the concentration from upstream to downstream and almost identical pattern was observed during both seasons. The source apportionment suggested that penta-BDE and to some extent octa-BDE commercial products were major sources of PBDEs in the study area. However, the sources of PAHs were mainly comprised of fossil fuels and biomass burning, followed by the petroleum products and their mixtures. The results of the ecological risk assessment indicated PBDEs contamination posed high ecological risks, while PAHs exhibited low or no ecological risks in the study area. Consistent with the environmental levels, the ecological risks of pollutants were relatively lower in the WS, compared to that in the DS. The results from this study would provide valuable baseline data and technical support for policy makers to protect the ecological environment of the Guanlan River. Image 1 • The concentrations of PBDEs and PAHs in the DS were higher than those in the WS. • The sources of PAHs were mainly comprised of fossil fuels and biomass burning. • Octa-BDE commercial products were major sources of PBDEs in the study area. • PBDEs posed high ecological risks, while PAHs posed low risks in the Guanlan River. • PBDEs and PAHs levels were affected by the content of TN, NH 4 -N, COD, BOD 5 and DO. Capsule: Rapidly urbanizing costal city Shenzhen is influencing the ecological resources of the Guanlan River through increasing the concentrations of PBDEs and PAHs. [ABSTRACT FROM AUTHOR]