The Zacapu shiner is differentiated from the other members of the N. calientis species complex by having 6, rarely 7, branched rays in the anal fin and 8 pelvic fin rays and by normally having 42 lateral line scales.

It has a yellowish to light brown body with a dark lateral stripe which widens to form a slightly convex part from near the pectoral fin origin to the dorsal fin origin, becoming narrower and darker towards the rear.

Zacapu Lagoon lies in the drainage basin of the Lerma River and is fed by 12 springs and tin the area near the springs there is clear, well vegetated water but in the rest of lake the water is turbid.

The introduction exotic carp species the common carp (Cyprinus carpio) and grass carp (Ctenopharyngodon idella) has led to the parasite Bothriocephalus acheilognathi being able to invade the lake and its indigenous fish assemblage, potentially including the Zapacu shiner.

The lake has also been affected by pollution and by water abstraction which has reduced its surface area to 32 hectares (79 acres).