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Aquatic ecosystems of North American deserts are frequently very restricted in area and tend to harbour very specialized species endemic to their restricted habitats. Small changes in environmental conditions of these specialized forms may jeopardize their persistence. A notable example of endemic and specialized species that may have been influenced by slight changes in its habitat is the Devils Hole pupfish (Cyprinodon diabolis), which occurs only in a small pool ecosystem in the Mojave Desert of the Southwestern United States. In this study, we use a computational fluid dynamic (CFD) model to examine the physical effects of climate change and local groundwater management on Devils Hole and combine those results with a conceptual ecological model to consider the impacts of those changes on annual recruitment of C.diabolis. The CFD model predicts water temperatures as a response to climate and water level, and the ecological model is used to determine the timing of tipping points that may encourage or suppress the annual recruitment of C.diabolis. The combination of interdisciplinary modelling approaches offers a method to quantify and compare the suitability of habitat under a range of management and climate scenarios. Our results show that the influence of water level on peak temperatures in Devils Hole (and on the ecosystem’s suitability for C.diabolis) is an order of magnitude greater than the influence of climate change. Copyright (c) 2015 John Wiley & Sons, Ltd.