Predicted no-effect concentration (PNEC) is often used in ecological risk assessment to determine low-risk concentrations for chemicals. In the present study, native marine species were selected for toxicity testing. The PNECs for three polycyclic aromatic hydrocarbons (PAHs), specifically phenanthrene (Phe), pyrene (Pyr), and benzo[a]pyrene (BaP), were derived from chronic and acute toxicity data with log-normal statistical methods. The achieved PNECs for Phe, Pyr, and BaP were 2.33, 1.09, and 0.011 μg/L, respectively. In Jinzhou Bay and the Shuangtaizi River Estuary of Liaodong Bay in the Bohai Sea, China, the surface water concentrations of the three PAHs were analyzed by gas chromatography-mass spectrometry. Based on two probabilistic ecological risk assessment (PERA) methods, namely probabilistic risk quotient and joint probability curve, the potential risk of Phe, Pyr, and BaP in Jinzhou Bay and Shuangtaizi River Estuary was assessed. The same order of ecological risk (BaP > Phe > Pyr) was found by both models. Our study considered regional characteristics of marine biota during the calculation of PNECs, and the PERA methods provided probabilities of potential ecological risks of chemicals. Within the study area, further research on BaP is required due to its high potential ecological risk.