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Comanche Springs pupfish are found in freshwater habitats in the San Solomon Spring System near Balmorhea, Texas. Other pupfishes in the Pecos River watershed occupy more saline waters, but those inhabited by Comanche Springs pupfish are relatively fresh. Comanche Springs pupfish are found in spring pools, spring-influenced marshes (ciénegas), and irrigation canals carrying spring waters. They evolved to be the only pupfish species in a given habitat; the presence of sheepshead minnow (Cyprinodon variegatus) is a threat to their persistence due to competition and hybridization.

Comanche Springs pupfish typically feed on pool bottoms or hard substrates. By volume, their diet consists primarily of algae, but by biomass accumulation, benthic invertebrates are the most important component. 

Territorial males guard eggs. Males exhibit three different behavior techniques around mating based on size: large males maintain and defend territories, average-sized males use satellite positioning around the periphery of territories, and small males that retain female coloring “sneak� into territories to quickly mate with females before escaping.

Baird and Girard described Comanche Springs pupfish based on material from Comanche springs, Pecos County, Texas. Comanche Springs pupfish are one of the most distinctive pupfishes, having a “peculiar� speckled blue male color pattern and lacking vertical black bars common to other pupfishes. The body shape of all individuals is streamlined for a pupfish, and the maximum size is approximately 50 millimeters (mm [1.97 inches (in)]) in standard length.

Comanche Springs pupfish typically live for one to two years in the wild, similar to other pupfishes.

Reproduction in Comanche Springs pupfish is possible year-round. Females become sexually mature at around five months old. Growth rates in males are faster. Spawning is typical of pupfish species, except that Comanche Springs pupfish have been observed to spawn in both slow-moving and moderately flowing waters. Female Comanche Springs pupfish lay eggs singly onto rocks or algal mats. They may lay up to 30 eggs per day (body size and eggs laid are correlated), which hatch in approximately five days.

Population size can be limited by total available habitat suitable for territories. Measured territories range from 0.14â€�0.225 square meters (1.5â€�2.4 square feet). Where suitable conditions exist, Comanche Springs pupfish populations can be numerous, in the tens of thousands. The life history of Comanche Springs pupfish means that large fluctuations in abundance can occur . Seasonal variation may be pronounced, with populations highest at the end of summer and lowest at the end of winter.