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This study investigated the occurrence of pesticides in typical coastal aquatic environment of St. Lucie Estuary and Indian River Lagoon. Multiple risk assessment methods, including deterministic screening and probabilistic risk assessment techniques, were performed to characterize potential ecological risks. The deterministic method indicated that pesticides exerted no risk to certain biotic groups (i.e. aquatic plants, fish, molluscs, and algae-moss-fungi), but did bring risks to larval insects and crustaceans. Results from the probabilistic risk assessment indicated significant ecological risks (acute and chronic) when organisms were exposed to the maximum and median concentrations detected, respectively. The potentially affected fraction of species (PAF) tends to be acutely impacted in the coastal aquatic environment. The PAF was likely impacted at chronic toxicity levels ranged from 17 to 20% for fipronil. Joint probability curve (JPC) analysis indicated that occurrence probability of concentrations exceeding the LC50 of the most sensitive 5% of species was 9–20%. Using the more conservative NOEC/LOEC values, there was an 80% probability that concentrations were high enough to negatively affect the most sensitive 5% of species, indicating significant risks for chronic toxicity. JPCs indicated a 3% probability of fipronil sulfone exceeding the LC50 concentrations for the most sensitive 5% of species at the same two sites. Results indicated that fipronil and its sulfone and sulfide metabolites may present significant risks to the typical coastal aquatic organisms. The research work was financially supported by One Hundred-Talent Plan of Chinese Academy of Sciences (CAS) (Y629041021).