|Nationwide biodiversity indicators based on landscape heterogeneity have been developed primarily for terrestrial, but not well for freshwater ecosystems. One plausible reason for this limitation may be due to the difficulty in fine discrimination of freshwater environments by remote sensing. In recent years, however, GIS vector data of freshwater land cover are classified in detail (i.e., rice paddy fields, other marshy wetlands, rivers, ponds, and lakes) in Japan. Using these GIS data, we developed an index for freshwater landscape heterogeneity with 1 km square as the spatial unit, which was named the "Satogawa" Index (SGI). The SGI formula consisted of two-component terms; one reflects the diversity of freshwater land covers, and the other represents their spatial shapes. To verify the usefulness of the SGI for freshwater biodiversity, we calculated the SGI at a central region in Japan and found significant relationships with the species richness of Odonata (dragonflies and damselflies) and freshwater fish. The amounts and spatial patterns of freshwater landscape elements by which the SGI was estimated were different among regions in Japan, but the SGI may be adapted to other regions as a surrogate of freshwater biodiversity. While many modifications are underway that may have negative consequences for freshwater biodiversity, land use has been changed for preventing flood damage and improving the freshwater environment. The SGI may assess the influences of the changes in land use on freshwater biodiversity and may identify the type and amount of lotic and lentic environment that should be supplemented to improve freshwater biodiversity at a certain location.