Benthic macroinvertebrates are sedentary and have an intermediate life span ranging from months to a few years. They play a key role as consumers in the food trophic structure by linking producers, top carnivores, and decomposers in aquatic communities. Therefore, they have been widely used for ecological assessment of aquatic ecosystem health in an integrative and continuous manner. In this study, we characterized benthic macroinvertebrate communities at reference sites, which are not disturbed. Benthic macroinvertebrates were collected seasonally with a Surber net at three different streams (Pocheon, Hongcheon, and Namhae). In addition, hydrological and physicochemical environmental factors including temperature, discharge, width, conductivity, dissolved oxygen and pH were also measured at each sampling site. Spatial and temporal differences of benthic macrointertebrate communities were analyzed based on community indices, functional guilds, etc. relating to their environmental factors. Multivariate analysis were used to characterize the relationships between communities and environmental factors. Benthic macroinvertebrates were significantly different among sampling sites reflecting differences of their environmental condition such as hydromorphological factors, meteorological factors, etc.