[4][5] The Comanche Springs pupfish stands out amongst cogeners due to the striking speckled color pattern of the males, as well as a more streamlined body shape and lack of vertical bars.

[6] Toyah Creek is intermittent, only flowing after heavy rainfall, and as a result only occasionally provides pupfish habitat.

[6] Most of the surviving habitat has been converted to a sixty-mile (97 km) network of interconnected concrete or earthen irrigation canals.

[9] Artificial refugia for the species have also been constructed at Balmorhea State Park, which contains San Solomon spring.

The entire head of this spring was converted into a concrete-lined swimming pool by the Civilian Conservation Corps in the 1930s, destroying the natural ciénega.

[7] 1996 saw the addition of a 2.5 ha (6.2 acres) ciénega within the grounds of the park, designed to replicate the appearance and functionality of the original.

Finally, from 2009 to 2010, a second small ciénega was built adjacent to the 1975 canal in order to replace the older, deteriorating structure.

[9] It occurs in water with lower salinity than that occupied by other pupfish species within the Pecos River system, suggesting a long interval of isolation.

[10] The diet of adult Comanche Springs pupfish consists mostly of filamentous algae as well as some snails,[9] while juveniles subsist solely on infusoria until they grow larger.

[9] Breeding behavior is similar in slow-moving water except that the territories are centered around a convenient landmark such as a rock or patch of plants.

[7] Modification of the Balmorhea area spring system starting in 1875 destroyed most of the natural marsh and stream habitat.

[6] Historic stocking of black bass species into the irrigation canals of the Phantom Cave Spring system likely severely impacted that population of pupfish.

[6] The Comanche Springs pupfish is further at risk simply due to the susceptibility of the small population to random catastrophic loss, such as a natural disaster.