Concentrations of industrial, agricultural and natural chemicals have been increasing in secondary effluents without their combined sub-lethal effects having been elucidated. In this study, two assays (the comet and acetylcholinesterase assays) were combined to evaluate the genotoxic and neurotoxic effects of effluent from the Noksan wastewater treatment plant (WWTP) on two local marine fish species (flounder and sea eel). The fish were exposed to WWTP secondary effluent that had been diluted with filtered seawater to final concentrations of 1%, 10% and 50%. Analysis of fish samples collected 3 and 5 days after exposure showed that DNA damage occurred in flounder exposed to 50% effluent and in sea eels exposed to 10% or 50% effluent. Furthermore, it was found that acetylcholinesterase (EC:3.1.1.7, AChE) activity decreased in both species when exposed to 10% effluent, indicating the presence of large amounts of genotoxic and neurotoxic chemicals in the effluent. Our results indicate that the comet and AChE assays are promising tools for biomonitoring of secondary effluents.