This study was carried out in Osan river to quantitatively investigate behavior of attacked microbial community (AMC) for enhancing self-purification process of river. We gained the results such as follows throughout long-term monitoring at in-situ river. The biomass of AMC had higher in the riffle than the almost stagnant pool and they were more developed in the riffle with high current velocity (HCV). Although the fast flowing current affects negatively to growth of the AMC during the early phase when the community gets attached to the benthic substrate, it was observed that it affected positively to their growth during the intermediate and later phase after the community is adapted to the substrate. When turbulence due to external pressure (storm or discharge of dam and reservoir) occurs, the degree of separation depends upon the flowing strength and the type of the external pressure. Since the community is not all separated, recovery is rather fast. Therefore, this study found that the degree of reduction of the pollutant by self-purification of the stream is depended upon the riverbed shape and the AMC contributes to self-purification positively or negatively in river. Therefore, the riverbed shape must be constructed in accordance with the characteristics of water quality in stream. Furthermore, the technique of installing the water channel structure appropriate for each section must be developed to maximize self-purification ability.