The distribution, source and potential ecosystem risk of 16 priority polycyclic aromatic hydrocarbons (PAHs) in Weihe River were estimated. In 2015 the mean values of ΣPAHs were 278.4 ng/L in water dissolved phase (WDP) and 1,340 ng/g dry weight (dw) in sediment, respectively. While in 2016 the mean concentrations of ΣPAHs reduced to 108.6 ng/L in WDP and 539.1 ng/g dw in sediment, respectively. The concentrations of PAHs in Weihe River were at a moderate level compared with other rivers in the world. Compared with the data in our previous study in 2014 and the data in other studies, the PAHs level in Weihe River in 2015 and 2016 decreased obviously. The PAHs concentrations in WDP and sediment samples from 8 sewage outlets discharging into Weihe River were much higher than those in Weihe River. Principal component analytical results indicated that coal combustion was the most important source of PAHs in Weihe River. The results suggested that Weihe River Comprehensive Treatment Project (WRCTP) played its role effectively in reducing PAHs pollution of Weihe River.