Longitudinal changes in community structure of macroinvertebrates were studied based on qualitative samples collected at 19 stations along 440 km reaches including headwater and floodplain reaches in the Tuul River, Mongolia, in June to July, 2005. Flow volume, channel geomorphology, water temperature, pH, EC, turbidity, alkalinity, DO and a set of inorganic nutrient concentrations were measured at each station. Compositional changes in habitat types, life forms and functional feeding groups of the macroinvertebrate community were analyzed and the stable isotope ratios of carbon and nitrogen were measured for major species of benthic animals, SPOM, BPOM and epilithon. Distinctive changes in the macroinvertebrate community occurred at stations with floodplains having still water habitats like backwaters in the abandoned channels. Longitudinal changes of the community were characterized by decrease in shredders and increase in collector-gatherers and filterers with increasing river size, which supported the classical model of RCC. The longitudinal changes in potential sources of their energy, however, indicated an importance of lenthic habitats sustaining primary production by phytoplankton. Changes in the variation of trophic levels of predatory macroinvertebrates and benthivorous fishes estimated by their isotopic signature were discussed in relation to the habitat structure and energy sources.