An approach to compare the toxicities employing the whole effluent toxicity (WET) test, using Daphnia magna and chemical analysis with GC/MS and ICP/MS, was conducted to the nine South Korean wastewater treatment plants (WWTPs). From the chemical analysis and bioassay experiments, heavy metals (i.e., Cu and Zn) were found to be the major compounds causing toxic effects toward D. magna. In the whole effluent toxicity (WET) tests using D. magna, toxicities were observed in 34% of the effluent samples. However, the biological toxic unit (TU) value showed a non-toxic response (i.e., 0 TU) in many samples despite the response indicated by the chemical TU values. This may be due to the species sensitivity, environmental parameters, mixture effects, and limitation of the chemical analyses.