Pupfish are a euryhaline group of fish and are able to withstand conditions such as elevated salinity, higher water temperatures, and lower dissolved oxygen, that many other fish cannot tolerate. The Pecos pupfish occurs in a variety of aquatic environments including wetlands, sinkholes, waterfowl impoundments, streams, springs, and the Pecos River mainstem. They prefer quiet water less than 2 meters (m) (6.56 feet (ft)) deep. A variety of underwater features such as crevices, boulders, large rocks, scattered pebbles, and aquatic plants provide topographic diversity throughout the range of the Pecos pupfish and are preferred for breeding substrate. Pecos pupfish become inactive over winter, when water temperatures drop below 10 °C (50 °F), and can be found in areas with dense vegetation and flocculent material (such as fine detritus or non-living organic matter) present in the substrate.

The percentage of males holding territory can vary year to year and is influenced by the amount of breeding and foraging habitat available (dependent on water levels) and that density of territorial males was highest in dense patches of aquatic vegetation, and lowest in flat silty areas with isolated rocks. Population size can be limited by total available habitat suitable for territories. Historical occurrence data show that Pecos pupfish have inhabited a variety of aquatic environments throughout their range, and that Pecos pupfish are able to move into previously unoccupied environments where conditions are suitable. It is reasonable to conclude that the Pecos pupfish colonized suitable uninhabited areas, possibly during periods of high-water flow when previously isolated areas become connected, allowing for expansion and contraction of ranges and abandonment and recolonization of streams as environmental and/or demographic conditions changed.

Critical Habitat

Critical habitat has been proposed for Pecos pupfish (89 FR 92744) that includes 136.12 river miles 219.06 river kilometers) of instream habitat (to the ordinary high water mark, not including riparian riparian
Definition of riparian habitat or riparian areas.

Learn more about riparian areas) and 26,555.54 acres (10,746.64 hectares) of lands that encompass numerous isolated sinkholes and wetland areas. The five areas proposed as critical habitat are: (1) Upper Pecos River Unit; (2) Salt Creek Wilderness Unit; (3) Bitter Lake Unit; (4) BLM Overflow Wetlands/ Bottomless Lakes Unit; and (5) Salt Creek (TX) Unit.

The following physical and biological features are essential to the conservation of Pecos pupfish (89 FR 92744):

1. Water quality parameters that support all life stages of the Pecos pupfish, including:
   1. Absence of pollutants, or a level of contaminants low enough that it does not negatively impact necessary water quality conditions for Pecos pupfish individuals;
   2. Salinity less than 35,000 mg/L;
   3. Temperature less than 42.7 °C (108.9 °F); and
   4. Dissolved oxygen greater than 2.5 mg/L.
2. Sufficient water quantity parameters that support all life stages of the Pecos pupfish, including:
   1. Permanent water in some area of habitat; and
   2. Water depth less than 2 m (6.56 ft) deep to allow for thermal refugia and breeding.
3. Presence of silt-free underwater features such as crevices, boulders, large rocks, scattered pebbles, and aquatic plants that are used for egg deposition.
4. Absence of nonnative invasive sheepshead minnow.

Pecos pupfish are opportunistic omnivores and vary their diet depending on available food sources; however, diet can be reflective of habitat, sex, and gut length. Stomach content analysis shows that Pecos pupfish consume diatom-detritus mixtures, animal material, filamentous algae, macrophytes, sand, and seeds.

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 “sneak” into territories to quickly mate with females before escaping.

Echelle and Echelle described Pecos pupfish based on material from across its range in Texas and New Mexico. Pecos pupfish are small, deep-bodied fish varying in body color from gray to-brown to iridescent blue. Females have blotched lateral bars on their sides. Pecos pupfish vary phenotypically amongst isolated habitat types, which may be advantageous for adapting to different food availability, dissolved oxygen availability, and salinity levels. Adults range in size from 28–46 millimeters (1.1–1.8 inches) in standard length. 

Most individuals in the wild live less than one year (Kodric-Brown 1977).

Adult Pecos pupfish breed in the late spring through early fall (May to September); however, breeding peaks when water temperatures are warm and food is abundant (late-June to July). Larvae hatch approximately one month after fertilization. Pecos pupfish are sexually mature at 20 mm (0.8 in) standard length, within a few months of hatching (Kodric-Brown 1983). Female Pecos pupfish lay individual eggs that adhere to spawning substrate, such as vegetation or rocks (Kodric-Brown 1977). Female Pecos pupfish lay an average of 10 eggs per day (Kodric-Brown 1977).