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Weihe River is a typical river located in the arid and semi-arid regions of Northwest China. In this study, the distribution and sources of 16 polycyclic aromatic hydrocarbons (PAHs) in Weihe River were investigated. The concentrations of Sigma PAHs ranged from 351 to 4427 ng/L with a mean value of 835.4 ng/L in water dissolved phase (WDP), from 3557 ng/L to 147,907 ng/L with a mean value of 20,780 ng /L in suspended particulate matter (SPM), and from 362 to 15,667 ng/g dry weight (dw) with a mean value of 2000 ng/g dw in sediment, respectively. The concentrations of PAHs in Weihe River were higher compared with other rivers in the world. In both WDP and sediment, the highest concentrations of Sigma PAHs were observed in the middle reach, while the lowest concentrations of Sigma PAHs were found in the lower reach. For SPM, however, the PAHs concentrations in the lower reach were highest and the PAHs concentrations in the upper reach were lowest. The ratios of anthracene/(anthracene + phenanthrene) and fluoranthene/(fluoranthene + pyrene) reflected a pattern of both pyrolytic and petrogenic input of PAHs in Weihe River. The potential ecosystem risk assessment indicated that harmful biological impairments occur frequently in Weihe River.