The Sacramento River's source waters rise in the volcanic plateaus and ranges of far northern California as two streams – the Upper Sacramento and Pit. The main stem rises in the shadow of Mount Shasta and flows south through the Klamath Mountains, past Mount Shasta, Dunsmuir and Lakehead for about 72 miles. However, the river's true headwaters lie far to the northeast, as the 315-mile Pit River, which is formed by streams flowing southwest from the Modoc Plateau. The two rivers join in the waters of Lake Shasta, a giant reservoir formed by the Shasta Dam. The upper Sacramento is only the main stem by name: the flow of the Pit into the lake, 4,269 cubic feet per second, is nearly four times that of the Sacramento's 1,191 cubic feet per second.
From the dam the Sacramento winds south through foothills and leaves the mountains near Redding, the first larger city on the river's course and second largest on its entire course. Many small and moderate-sized tributaries join the river from both east and west including Clear, Cottonwood, Cow, Thomes, Ash and Battle Creeks. As the river meanders into the Central Valley a large portion of its flow is diverted into a pair of irrigation canals at Red Bluff. The Sacramento continues south, receiving Mill Creek near Tehama, and Stony and Big Chico creeks a bit southwest of Chico. The river then passes Colusa, and receives Butte Creek about 3 miles west of the Sutter Buttes, a group of isolated volcanic hills in the middle of the Sacramento Valley.
Twenty-five miles southeast of Colusa near Fremont Landing, the Sacramento incorporates the flow of its largest tributary, the Feather River, which descends from the Sierra Nevada to the northeast. About 10 miles downstream, it flows into the city of Sacramento, California and receives the American River, its second largest tributary. Here the river splits into two: the main stem and the artificial Sacramento Deep Water Ship Channel. Both waterways continue south through the lowlands, eventually to rejoin in the estuary of the Sacramento-San Joaquin Delta near Rio Vista.
The mouth of the Sacramento is on Suisun Bay near Antioch, where it combines with the San Joaquin River, south of the Montezuma Hills. The Sacramento is nearly a mile wide at its mouth. The joined waters then flow west through the tidal marshes of Suisun Bay, the Carquinez Strait, San Pablo Bay and San Francisco Bay, whereupon the river's waters finally join the Pacific in the Golden Gate just to the north of San Francisco.