The purpose of this study was to treat complex wastewater consisting of domestic wastewater, tobacco processing and building materials washings. The proposed multi-level bioreactor consists of a biopond-biofilter, anoxic/aerobic (A/O) fluidized beds and a photoautotrophic system. The results show that when the hydraulic load of the bioreactor was 200m3/d, it successfully and simultaneously removed the organic matter and metals. When the bioreactor was in a relatively steady-state condition, the overall average organic matter and metals removal efficiencies are as follows, COD (89%), UV245 nm-matter (91%), Cu (78%), Zn (79%) and Fe (84%). The growth conditions of the native bacterial habitat were improved, which resulted from the increase of the in bacterial diversity under the rejuvenated conditions induced by the bioreactor. The results demonstrate that the multi-level bioreactor, without a sludge treatment system, can remove heterogeneous organic matter and metals from wastewater.