The removal of organic matter is a fundamental process in sewage treatment. Small scale sewage treatment plants, in particular, demand low cost and easy operation and maintenance. It is said that a hybrid water treatment system incorporating more physicochemical than biological processes for the removal of organic matter can be more convenient and incur less cost compared with a conventional activated sludge systems. Therefore, in this study, we propose a hybrid water treatment system equipped with a jet mixed separator (JMS), which is a type of pre-coagulation-sedimentation tank, and an aerobic moving bed biofilter (MBB). We then investigate the behaviour of particulate and soluble organic matter and the oxygen consumption by the biofilm in this hybrid system. The results indicate that the addition of the poly silicate iron coagulant in JMS increases the quantity of removed organic matter by approximately 30% compared with the process without coagulant, and that the majority of the removed organic matter is soluble. That is, the JMS effectively reduced the organic matter that can be eliminated only by biological treatment, and not by mechanical treatment. The residual organic matter of JMS was removed from the liquid phase within an hour, which is the hydraulic retention time (HRT) of MBB, and the removed soluble organic matter was almost perfectly biodegraded in the biofilm within a day. That is, MBB could continuously operate without excess growth of microorganisms as long as the filtering was working properly. Thus, the hybrid system is expected to maximize the performance of MBB.