Three channel reaches with different habitat characteristics were selected to test the variability in community structure of benthic macroinvertebrates by comparing the relative abundance of functional feeding groups among the reaches. The important factors influencing the spatial and temporal organization of community structure were explored using nonmetric multidimensional scaling (NMS). The habitat characteristics in the reaches were different in terms of habitat type, hydrological factors, and substrate composition. The first headwater reach was classified as a step-pool reach with similar relative areas of riffle and pool habitats. The second mid-reach and the third down reach had greater areas of pool habitat followed by runs and riffles whose proportions were similar between the latter two reaches. The relative abundances of functional feeding groups were different among the surveyed reaches. Gammarid shredders predominated in the upper reach, and chironomid collector-gatherers and collector-filterers were in greater abundance in the two lower reaches. The proportions of gammarids were minor in the mid and downstream reaches. NMS ordination indicated that the proportion of substrates<8 mm, discharge, and water depth mainly determined the spatial and temporal distribution of samples based on the macroinvertebrate community in the study reaches. These results suggest that different habitat characteristics result in a distinct community structure in each reach.