Eutrophication increases the amount of dissolved organic matter (DOM) utilized by various microbial food web components mediated by bacteria. This process makes the contribution of the microbial food web larger in matter cycling and energy flow of aquatic ecosystem. At the same time, it can affect zooplankton community, particularly through rotifers, because they are main predators in microbial food web as well as preys for predacious zooplankton. Therefore, it is essential to estimate the role of rotifers as selective predators for understanding the interactions among DOM, microbial loop, and zooplankton community. In the present study, we selected six reservoirs which have various quantity and quality of DOM, and monitored seasonal changes of zooplankton community and DOM characteristics which was measured by three-dimensional fluorescence excitation-emission matrices (EEM). We focused on the tendency of bacterial changes with that of DOM composition, and their interactions with rotifers community. In addition, we estimated the relationship between rotifers and microbial food web components from the view point of selective feeding behavior of rotifers based on the concept of functional groups categorized by rotifers masticatory apparatus, trophi.