It has its origin in Cibola County, New Mexico, in the Zuñi Mountains at the Continental Divide.

The river flows off the western slopes of the Zuñi Mountains in a generally southwesterly direction through the Zuni Indian Reservation to join the Little Colorado River in eastern Arizona.

[6] The river is intermittent, drying up during drought periods, and often during most of the winter, except where there are perennial springs that give it surface flow for a short distance.

[3] The Zuni Basin is home to the Moreno Hill Formation where fossils from the later Cretaceous 92 Mya.

Fossils include dinosaurs like Zuniceratops and Suskityrannus (Zuni Coelurosaur).