Twelve polybrominated diphenyl ethers (PBDEs) were measured in water, suspended particulate matter (SPM) and sediment samples during dry season (DS) and wet season (WS), to explain the spatiotemporal distribution, congener profiles, sources and risks of the pollutants in four reservoirs (A-D) and their tributaries of a large city in South China. The concentration of ∑12PBDEs ranged from 0.46 to 2.27 ng/L (average: 1.41 ng/L) in water during WS, and from 0.70 to 13.04 ng/L (3.77 ng/L) during DS. Meanwhile, the content of ∑12PBDEs ranged from 9.71 to 364.14 ng/g dry weight (the same below) (170.23 ng/g) in SPM during WS, and from 53.48 to 1043.69 ng/g (313.37 ng/g) during DS. The content of ∑11PBDEs (excluding BDE-209) ranged from 24.70 to 222.75 ng/g (85.86 ng/g), while that of BDE-209 ranged from 4.74 to 31053.11 ng/g (6307.93 ng/g) in sediment during WS. ∑12PBDEs during DS were significantly higher than WS. Source apportionment suggested that commercial penta-, octa- and deca-BDEs were major compositions of PBDEs, resulting mainly from atmospheric deposition, wastewater discharge and external water diversion project. Among the related enterprises, attentions should be paid to electronic equipment manufacturing factories in this study area. The risk assessment indicated low ecological and insignificant human health risks posed by PBDEs in water, but the risk of PBDEs (especially BDE-209) in sediment and SPM was of particular concern. The present study would provide important data and support for the control of PBDEs in natural drinking water sources.