As the wastewater treatment process is directly related to the environmental process, its technology should be accepted to the public. Substances included in wastewater are so variable such as not only biological origin but also xenobiotic that their physical and chemical properties are very much complicated. Their biological treatment process is to utilize the versatile characteristics of microbes. Degradation pathway of a target chemical is generally composed of many enzymatic reactions so that one microbial species does not necessarily produce all enzymes for the reactions, which implies the necessity of constructing microbial consortium. During the startup of the biological wastewater treatment process the acclimatization process, which is considered to prepare microbes carrying plasmid encoding the necessary enzymes and also to construct microbial consortium, is needed. Taking the reception by the public into consideration, microbial preparation will not be done by a so-called artificial genetic manipulation but utilizing the gene transfer phenomena observed in the natural environment. In the present paper, by setting the above two views as a steering concept a composite microbial system consisting of porous carriers aiming at the simultaneous removal of carbonaceous and nitrogenous compounds, and a system for degrading a xenobiotic compound are examined. In addition, gene transfer which may appear in the wastewater treatment system is also discussed.