Water samples were collected from wastewater treatment plant (WWTP), drain water (DW), major tributaries (MT), and main course of the Yangtze River (MY) in areas of three industrial parks (IPs) in Chongqing city in the Three Gorges Reservoir (TGR). Sixteen EPA priority polycyclic aromatic hydrocarbon (PAH) pollutants were quantified to identify the effects of industrial activities on water quality of the TGR. The results showed that 11 individual PAHs were quantified and 5 PAHs (naphthalene (Nap), acenaphthylene (Acy), benzo[k]fluoranthene (BkF), indeno[1,2,3-cd]pyrene (InP), and benzo[g,h,i]perylene (BgP)) were under detection limits in all of the water samples. Three-ring and four-ring PAHs were the most detected PAHs. Concentrations of individual PAHs were in the range of not detected (nd) to 24.3ng/L. Total PAH concentrations for each site ranged from nd to 42.9ng/L and were lower compared to those in other studies. The mean PAH concentrations for sites WWTP, DW, MT, and MY showed as follows: DW (25.9ng/L) > MY (15.5ng/L) > MT (14.0ng/L) > WWTP (9.3ng/L), and DW contains the highest PAH concentrations. Source identification ratios showed that petroleum and combustion of biomass coal and petroleum were the main sources of PAHs. The results of potential ecosystem risk assessment indicated that, although PAH concentrations in MT and MY are likely harmless to ecosystem, contaminations of PAHs in DW were listed as middle levels and some management strategies and remediation actions, like strengthen clean production processes and banning illegal sewage discharging activities, etc., should be taken to lighten the ecosystem risk caused by PAHs especially risks caused by water discharging drains.