Headwater streams are the main sources of water sediment and organic material for downstream reaches and their small catchments coupled terrestrial-aquatic linkages. Because headwater streams provide valuable habitats for unique and diverse assemblages of aquatic fauna, they are also essential for sustaining the structure and function of the watersheds. Therefore, it has been recently supported that headwaters are important areas for maintaining biodiversity. In this study, we surveyed four different headwater streams in different watersheds to characterize differences of benthic macroinvertebrate assemblages among study streams. Benthic macroinvertebrates were collected seasonally with a Surber net at four different streams. In addition, hydrological and physicochemical environmental factors including temperature, discharge, width, conductivity, dissolved oxygen and pH were also measured at each sampling site. Community indices were used to differentiate spatiotemporal changes of macrointertebrate communities. Multivariate analysis were used to characterize the relationships between communities and environmental factors. Differences of their environmental condition such as meteorological factors and stream hydromorphological factors were reflected in the ordination with macroinvertebrate communities.