The species occurs in wide, fairly shallow, flowing water, often less than 0.5 meter (1.6 feet) deep.  It is associated with river bottoms possessing sandy substrates, though they have occasionally been found in areas of silt over sand or sand and small gravel.  Smalleye shiners are known to forage in sandy sediments, which may explain their preference for sandy substrates.  Smalleye shiners, like other native fishes of the upper Brazos River, are relatively tolerant of the highly variable water conditions typical of arid prairie streams, including naturally elevated temperature, salinity, and turbidity, and low dissolved oxygen.  However, environmentally induced mortality resulting from low dissolved oxygen in isolated pools is known to occur, and mortality may also occur from naturally occurring salt plumes.  It’s estimated that an average of 6.43 cubic meters per second (227 cubic feet per second) of water discharge is necessary to sustain populations of smalleye shiners during the summer.  An unobstructed free-flowing reach length of greater than 275 kilometers (171 miles) is recommended for long-term survival of the species, based on comparisons with related minnows. 

The smalleye shiner is a generalist feeder, relying on a variety of food items to sustain growth and reproduction.  Averaged over one year, the gut contents (by weight) of smalleye shiners consist primarily of sand-silt (42 percent), invertebrates (38 percent), detritus (14 percent), and plant material (5 percent).  However, feeding habits vary by season with most of the sand-silt gut contents occurring mid-summer through fall, plant gut contents during spring and summer, and detritus gut contents during spring and fall.  The prevalence of sand-silt and detritus in the gut of the smalleye shiner suggests that this species forages among sediments on the river bottom throughout the year. 

The smalleye shiner is a small, pale minnow, measuring 3.5 to 4.4 centimeters (1.4 to 1.7 inches) endemic to the Brazos River.

The smalleye shiner appears as a light olive-green, with a dark outline to the scales on the back.  Its underside is white.  The minnow has a pale silver strip running down the side, which is more apparent on the front half than back.  The smalleye shiner can appear to have small, faint dots along its top or be checkered along the edges of its stomach.