Odonata species are sensitive to environmental changes, particularly those caused by humans, and provide valuable ecosystem services as intermediate predators in food webs. We aimed: (i) to investigate the distribution patterns of Odonata in streams on a nationwide scale across South Korea; (ii) to evaluate the relationships between the distribution patterns of odonates and their environmental conditions; and (iii) to identify indicator species and the most significant environmental factors affecting their distributions. Samples were collected from 965 sampling sites in streams across South Korea. We also measured 34 environmental variables grouped into six categories: geography, meteorology, land use, substrate composition, hydrology, and physicochemistry. A total of 83 taxa belonging to 10 families of Odonata were recorded in the dataset. Among them, eight species displayed high abundances and incidences. Self-organizing map (SOM) classified sampling sites into seven clusters (A–G) which could be divided into two distinct groups (A–C and D–G) according to the similarities of their odonate assemblages. Clusters A–C were characterized by members of the suborder Anisoptera, whereas clusters D–G were characterized by the suborder Zygoptera. Non-metric multidimensional scaling (NMDS) identified forest (%), altitude, and cobble (%) in substrata as the most influential environmental factors determining odonate assemblage compositions. Our results emphasize the importance of habitat heterogeneity by demonstrating its effect on odonate assemblages.