A notable attribute of the desert pupfish is their ability to survive in environments of extreme salinity, pH, and temperature, and low oxygen content.

The desert pupfish mates in a characteristic fashion, wherein compatible males and females will come in contact and collectively jerk in an s-shape.

[5][6] Historically, the desert pupfish occurred in the drainage basins of the Gila, Santa Cruz, San Pedro, and Salt, and lower Colorado River.

[9][13] The desert pupfish is a small fish that is typically less than 7.62 cm (3 in) long; males are larger than females and generally have more vivid markings, especially during breeding seasons.

Females and juveniles typically have tan or olive backs and silvery sides with narrow, dark vertical bars situated laterally.

Pupfish typically prefer clear waters with either rooted or unattached aquatic plants, restricted surface flow, or sand-silt substrates, and will do well if their habitats have little vegetation apart from mats of benthic algae.

Due to both habitat destruction and species reclassification, however, the desert pupfish has a smaller territory distribution than previously thought.

[citation needed] As of 2010, naturally occurring populations of the desert pupfish are restricted in the United States to two tributaries and various shoreline pools and irrigation drains of the Salton Sea in California.

[19] Pupfish show some dietary preference towards nektonic organisms, going so far as to suppress or even eliminate local populations of mosquitoes.

[18][19][20][21][22] Exposed eggs are typically and readily eaten by other pupfish of the same species if not laid in an inconspicuous area, while mobile fry are ignored unless adults are very hungry.

Under conditions of abundant food and suitable temperature, the desert pupfish may become sexually mature as early as six weeks of age.

The former occurs in large habitats with high primary productivity, limited breeding substrates, and high population density, and it is the most common; the latter occurs in habitats with low primary productivity, abundant breeding substrates, and low population density.

[27][28] During the breeding season, male pupfish establish and actively patrol and defend individual territories that are typically less than 1 meter deep and 1–2 meters in area; these territories vary in size based on individual fish size, density of other male pupfish, and water temperature, and are associated with small structures or incongruities of substrate.

When a female is ready to spawn, she will leave the school to enter the territory of an attractive male, and the mating process described above will commence.

Though the pair usually separates to leave one fertilized egg in the substrate, the female will very occasionally immediately form an S-shape and both fish will again perform the jerking sequence.

In addition to these anthropogenic effects, desert pupfish have also been threatened by disease and predation due to invasive and nonnative species.

The most recent decline of desert pupfish have shown to be correlated with environmental competition, predation and behavioral activities that interfere with reproduction, though the direct effects of these factors are unknown.

[15][35] Various management factors have been suggested as beneficial towards saving the desert pupfish, including the control and management of exotic and invasive species in pupfish habitats; the maintenance of water levels, quality, and the proper functioning condition of ponds, springs, and drains; the restoration and enhancement of degraded habitat; and the establishment of large primary refuge populations for each group of wild C.