Abstract
Freshwater biodiversity is highly endangered and faces increasing threats worldwide. To be complete, regional plans that identify critical areas for conservation must capture representative components of freshwater biodiversity as well as rare and endangered species. We present a spatially hierarchical approach to classify freshwater systems to create a coarse filter to capture representative freshwater biodiversity in regional conservation plans. The classification framework has four levels that we described using abiotic factors within a zoogeographic context and mapped in a geographic information system. Methods to classify and map units are flexible and can be automated where high‐quality spatial data exist, or can be manually developed where such data are not available. Products include a spatially comprehensive inventory of mapped and classified units that can be used remotely to characterize regional patterns of aquatic ecosystems. We provide examples of classification procedures in data‐rich and data‐poor regions from the Columbia River Basin in the Pacific Northwest of North America and the upper Paraguay River in central South America. The approach, which has been applied in North, Central, and South America, provides a relatively rapid and pragmatic way to account for representative freshwater biodiversity at scales appropriate to regional assessments.