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Emergent sandbar maps of the Missouri River produced by Northern Prairie Wildlife Research Center continue to be used by the U.S. Army Corps of Engineers and U.S. Fish and Wildlife Service to monitor and manage critical breeding habitat for the endangered Interior population of least terns and the threatened Northern Great Plains population of piping plovers. These maps have been created and refined annually for over ten years. Using high spatial resolution satellite imagery we have developed and continue to refine a database of spectral and spatial properties of potential habitat categories that are classified using a probability-based method. We have focused on increasing automation of these methods to further improve the cost-effectiveness of producing multiple maps during a season that capture temporal variability of available habitat on low-relief emergent sandbars that is related to variation in river discharge.