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Although riparian and aquatic ecosystems make up a small fraction of the area in arid and semi-arid lands, they are critical for the survival of desert life. There are, however, few compendia of efforts to define the quantity of water needed to maintain these ecosystems and understand the risks and stressors to them. Through our analysis we found that 62% of the rivers examined in the deserts of the U.S. and Mexico have had just one study over the past four decades and 67% of studies used qualitative methods. Furthermore, only one-third of the 312 species catalogued in our work have been studied more than once and only 5% have been considered five or more times. The most common risks or stressors to riparian and aquatic species were engineered structures, invasive species, and altered flows; and while 10% of studies included climate stressor, climate change impacts were infrequently examined. Ultimately, we found that although research has been conducted across the desert watersheds of the U.S. and Mexico, there are significant gaps in our knowledge of basic data such as the location and extent of perennial and intermittent streams, let alone studies of environmental flow needs. (C) 2017 Elsevier Ltd. All rights reserved.