Background: Phenol and nitrophenol are common compounds found in different types of industrial wastewater known as serious threats to human health and natural environment. In this study, Daphnia magna was used to evaluate the effectiveness of "baffle fixes film up flow sludge blanket filtration" (BFUSBF) system in elimination of phenolic compounds from water. Methods: D. magna cultures were used as toxicity index of phenol and 2,4-DNP mixtures after treatment by a pilot BFUSBF system which consisted of baffle in anoxic section and biofilm in aerobic sections. Initial concentrations were 312 mg/L phenol and 288 mg/L 2,4-dinitrophenol (2,4-DNP). Results: Bioassay tests showed that D. magna was influenced by the toxicity of phenol and 2,4 DNP mixtures. The comparison between the toxicity of initial phenol and 2,4-DNP mixtures and the output toxic unit (TU) derived from BFUSBF treatment system showed that the TU of the effluent from BFUSBF reactor was much lower than that of the solution that entered the reactor. Conclusion: Based on the acute toxicity test, BFUSBF process could reduce phenol and 2,4-DNP in aqueous solutions. Therefore, it is possible to use BFUSBF process as an appropriate treatment option for wastewaters containing phenolic compounds.