This study analyzed the relationship between the community structure of benthic macroinvertebrates and habitat changes in open estuaries among the sites included in the national estuary monitoring program. The estuary survey was conducted under the “Guidelines for Investigation and Evaluation of Biometric Networks” and classified by sea area, 80 places in the East Sea, 102 places in the South Sea, and 19 places in the West Sea were investigated. In a total of 201 open estuaries, benthic macroinvertebrates were identified with 4 phyla, 9 classes, 41 orders, 139 families, 269 species and 196 species in the East Sea, 182 species in the South Sea, and 90 species in the West Sea. The highest population densities were Insecta in the East Sea, the Malacostraca in the South Sea, and the Annelida in the West Sea. Through SIMPER analysis, species contributing to the similarity of benthic macroinvertebrates communities in each sea area were identified. Some species greatly influenced the similarity of clusters. The benthic community in the East Sea was affected by the salinity, so the contribution rate of freshwater species was high. On the other hand, the benthic communities of the South and West Seas showed species compositions are influenced by the substrate composition. As results, the benthic macroinvertebrate community in Korean estuaries was impacted by salinity and substrate simultaneously, and the close relationship with geographical distance was not observed. The result of this study is expected to be used to respond to environmental changes by identifying and predicting changes in the diversity and distribution of benthic macroinvertebrates in Korea estuaries.