[7] Rising south of Cone Peak, within the Ventana Wilderness of Los Padres National Forest in Monterey County,[8] the Nacimiento River flows southeast through a rugged canyon before emerging in a large alluvial valley within Fort Hunter Liggett.

After being joined by Stony Creek about 15 miles (24 km) west of Lockwood, the Nacimiento River flows through a series of remote canyons and narrow valleys along the eastern foothills of the Santa Lucia Range.

Except for its uppermost reaches and headwaters, as well as the short stretch below Nacimiento Dam, much of the river is dry in summer and fall, although perennial pools abound.

Tributaries to the upper river include Little Burnett, Tabacco, Salmon, Las Berros, San Miguel, Stony, El Piojo, Waller, and Sapaque Creeks.

Streams which flow into the lower river include Las Tablas, Franklin, Town, Dip, Snake, and Kavanaugh creeks.

Valley floors consist of a mix of native bunchgrass and needlegrass as well as non-native annual grasses seeded for grazing.