Its native habitat includes desert marshes with water temperatures up to 33 °C in the summer and layers of ice during the winter.

[4] The water in some areas has four times the salt content of the ocean, as well as low oxygen.

[6] When they were transferred to a safer location by Phil Pister, the entire global population of this pupfish was contained in two buckets.

In 2021, another population of Owens pupfish was established at the River Spring Lakes Ecological Reserve in Mono County, California.

The plant clogs the habitat and collects detritus, which eliminates the pupfish's breeding substrates.

They include predatory fish such as largemouth bass (Micropterus salmoides), smallmouth bass (Micropterus dolomieu), brown trout (Salmo trutta), and bluegill (Lepomis macrochirus), as well as crayfish (Pacifastacus leniusculus) and bullfrogs (Rana catesbeiana).