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Captive propagation of desert spring fishes, whether for conservation or research, is often difficult, given the unique and often challenging environments these fish utilize in nature. High temperatures, low dissolved oxygen, minimal water flow, and highly variable lighting are some conditions a researcher might need to recreate to simulate their natural environments. Here we describe a mesocosm-scale habitat created to maintain hybrid Devils Hole x Ash Meadows Amargosa Pupfish (Cyprinodon diabolis x C. nevadensis mionectes) under conditions similar to those found in Devils Hole, Nevada. This 13,000-L system utilized flow control and natural processes to maintain these conditions rather than utilizing complex and expensive automation. We designed a rotating solar collector to control natural sunlight, a biological reactor to consume oxygen while buffering water quality, and a reverse-daylight photosynthesis sump system to stabilize nighttime pH and swings in dissolved oxygen levels. This system successfully controlled many desired parameters and helped inform development of a larger, more permanent desert fish conservation facility at the U.S. Fish and Wildlife Service’s Ash Meadows National Wildlife Refuge, Nevada. For others who need to raise fish from unique habitats, many components of the scalable and modular design of this system can be adapted at reasonable cost.