It is a tributary of the Río Grande de Santiago in the southern Sierra Madre Occidental.

The Huaynamota drains a basin of 17,265 km2, which covers parts of the states of Nayarit, Durango, Jalisco, and Zacatecas.

The basin of the San Pedro Mezquital River bounds it on the west and northwest.

The basin has an average annual rainfall of 600 mm, which mostly falls during the June-to-October summer wet season.

The Cora people live in the western basin, including the valley of the Jesús María River.