The Topeka shiner is a small minnow with an olive-yellow back, dark-edged scales, and silvery-white sides and belly. A dark stripe runs along the fish's sides and extends onto the head. All of the fins are plain except for the tail fin, which has a triangular black spot at its base. The anal fin has 6 to 8 rays, usually 7. There is a dark stripe on the back in front of the dorsal fin. The upper jaw does not extend beyond the front of the eye.
Breeding males have orange-red fins and orange-tinted heads and bodies. Numerous bumps are located on the snout, the top of the head, most of the body, and along the rays of some of the fins. The bumps are largest and most numerous around the head.