The occurrence, distribution, and ecological risk assessment of 15 polycyclic aromatic hydrocarbons (PAHs) were investigated in the Dongjin River water system from December 2010 to October 2012. Among the detected PAHs, the mean concentration of acenaphthylene was the highest. Other PAHs were detected at very low concentrations. The detection frequencies and concentrations of the 15 PAHs were generally higher in the winter season, indicating low water flow conditions and low temperature. The results of a survey of the origin of the PAHs using the Phe/Ant ratio and Fla/Pyr ratio clearly indicated a pyrogenic source. The risk quotient (RQ) values for the 15 PAHs in the Dongjin River water system were below 0.01–0.1, indicating little risk to the relevant sensitive aquatic organisms, including green algae and daphnids, by the target compounds. In particular, the RQ values of most of PAHs exceeded 0.1 for fish in all of the seasons at most of the sampling sites, which indicated that the fish were exposed to medium risk.