Ecoregions are defined by the World Wildlife Fund (WWF) as "relatively large units of land or water containing a distinct assemblage of natural communities and species, with boundaries that approximate the original extent of natural communities prior to major land-use change". Freshwater ecoregions represents the freshwater habitats of a particular geographic area, including rivers, streams, lakes, and wetlands. Freshwater ecoregions are distinct from terrestrial ecoregions, which identify biotic communities of the land, and marine ecoregions, which are biotic communities of the oceans.

The WWF identifies seven major habitat types of freshwater ecoregions: Large rivers, large river headwaters, large river deltas, small rivers, large lakes, small lakes, and xeric basins.

Several freshwater ecoregions are listed in the Global 200, the WWF's priority ecoregions for conservation of biodiversity.