With their unique geographical characteristics, semi-closed narrow bays are important places for human survival but vulnerable to pollution. Because pollutants (polycyclic aromatic hydrocarbons, PAHs) migrate and undergo transformation through a dynamic mechanism in bays of this type, environmental authorities have formulated a series of effective measures for pollution prevention and control, but these are difficult to realize. Based on monitoring and historical data, a multiphase-coupled hydrodynamic model combined with a carcinogenic risk-assessment model was able to solve the challenging environmental problem. Results showed that the hydrodynamic condition in the semi-closed narrow bay was very complex. A weaker hydrodynamic force had an adverse influence on the diffusion of pollutants, further amplified in part by the head of the semi-closed narrow bay, resulting in a higher ecological risk. The prediction results indicated that the total amount of PAHs transported from seawater to sediments was about 4.7 × 10¹³ ng/year, which might cause serious threats to aquaculture or human health.