Lake Taihu provides vital ecological services for humans in China; it receives a great deal of attention regarding its ecological and environmental conditions. In this study, the ecological risks of eight individual polycyclic aromatic hydrocarbons (PAHs) in water were assessed using probabilistic distributions of the hazard quotient based on Monte Carlo simulation. The results show that the 95th percentile of the hazard quotients ranged from 0.00074 to 2.831, and the ecological risk of Flua was highest, followed by, in descending order of risk, B[a]P > Pyr > Ant> Phe > Flu > Ace > Chr. The probabilities of hazard quotients exceeding a decision criteria of 0.3 were 18.09%, 6.51%, 3.76%, and 2.85% for Flua, B[a]P, Pyr, and Ant, respectively, indicating their potential ecological risks to aquatic organisms. The spatial distribution of hazard quotients for these four individual PAHs with potential ecological risk were obtained using Geographic Information System (GIS), and similar spatial distribution patterns were also observed in the lake. The highest ecological risks of these four individual PAHs to aquatic organisms were found in Meiliang Bay, followed by Gonghu Bay and Xukou Bay. The uncertainty within the ecological risk assessment was also discussed.