It originates in the Bosque de la Primavera in Jalisco, 23 km to the west of state capital Guadalajara; flows through the city of Ameca; and then forms the boundary between Jalisco and Nayarit on its way to the Pacific Ocean, where it drains into the Bahía de Banderas at Puerto Vallarta, Jalisco.

Its main tributaries are the Ahuacatlán and Amatlán de Cañas.

The Ameca has been dammed just north of the town of La Vega, Jalisco, forming a reservoir, the Lago La Vega which extends northward to the town of Teuchitlán.

[3][4][5] The butterfly splitfin and banded allotoca were also thought to be extinct in the wild, but have since been rediscovered.

[3][8] A reintroduction project for the shiner and Tequila splitfin was initiated in 2015.