Not far downstream from its confluence with the American River, the Sacramento River joins the San Joaquin River in the Sacramento River Delta, which empties into Suisun Bay, the northern arm of San Francisco Bay. It is the third largest river by volume emptying into the Pacific Ocean in the Continental United States, behind only the Columbia River and the Colorado River.
The chief tributaries of the Sacramento River are the Pit, Feather, McCloud and American rivers. The Pit River is the longest of these, but the Feather and American rivers carry larger volumes of water. The Pit River's watershed formerly included Goose Lake, and still does during rare periods of high water.
According to Mt. Shasta Recreation & Parks District, the designated headwaters of the Sacramento River are at about 3600 feet (1100 m) elevation in Mount Shasta City Park (). The USGS cites the river's source as the confluence of the South Fork Sacramento River and Middle Fork Sacramento River.
Big Springs feeds Big Springs Creek which flows south into Lake Siskiyou. However, feeding Lake Siskiyou from the west are the North, Middle, and South Forks of the Sacramento River which bring water from much higher elevations, including from Castle Lake (elevation The South Fork originates at 5,912 feet (1,802 m) at Cedar Lake the Middle Fork originates at 6,359 feet (1,938 m) in several headwater streams near Chipmunk Lake and the North Fork originates from springs at about 7,900 feet (2,408 m) near .
These various headwaters flow into Lake Siskiyou near the city of Mt. Shasta. From there the river flows generally south, closely followed by Interstate 5. Just north of the city of Redding, the river is impounded by Shasta Dam, which creates a reservoir called Shasta Lake. The Pit River and McCloud River tributaries join the Sacramento in Shasta Lake.
Below Shasta Dam, the Sacramento River continues to flow south, passing Redding and collecting many small streams. The river passes by Red Bluff and near Chico. It bends slightly west around Sutter Buttes, then collects the tributary waters of the Feather River just north of the City of Sacramento. In Sacramento, the American River joins the Sacramento River.
During the Memorial Day weekend, and again in mid summer each year Red Bluff Diversion Dam creates Lake Red Bluff. Lake Red Bluff supplies water to the Tehama-Colusa and Corning Canals providing water for 100,019 acres, and $88,529,000 worth of crops. Lake Red Bluff also provides recreational opportunities in the form of sailing, jet skiing, water skiing, and drag boat racing. Tourism and recreation revenues are important part of the region’s economy. Lake Red Bluff is of great environmental importance since the Tehama-Colusa Canal supplied water for 20,000 acres of the Sacramento Valley (wildlife) Refuges.
Below Sacramento, the river enters the Sacramento River Delta, where it is joined by the San Joaquin River. The combined waters then exit into Suisun Bay, San Pablo Bay, and San Francisco Bay, before finally entering the Pacific Ocean at the Golden Gate.
Marine animals such as whales and sea lions are occasionally found far inland after navigating the river for food or refuge and then losing track of how to get back to the Pacific Ocean. In October 1985 a humpback whale affectionately named "Humphrey the humpbacked whale" by television media traveled up the Sacramento River before being rescued. Rescuers downstream broadcast sounds of humpback whales feeding to draw the whale back to the ocean.
On May 14, 2007, two humpback whales were spotted by media and onlookers traveling the deep waters near Rio Vista. The duo, generally believed to be mother and calf (Delta, the mother and Dawn, her calf), continued to swim upstream to the deep water ship channel near West Sacramento, about inland. There was concern because the whales had been injured, perhaps by a boat's propeller or keel, leaving a gash in each whale's skin. The whales were carefully inspected by biologists and injected with antibiotics to help prevent infection. After days of efforts to lure (or frighten) the whales in the direction of the ocean, the whales eventually made their way south into San Francisco Bay, where they lingered for several days. By May 30, 2007, the cow and calf apparently slipped out unnoticed under the Golden Gate Bridge into the Pacific Ocean, likely under cover of night.
The Sacramento Area Flood Control Agency is a Joint Powers agency tasked with keeping the Sacramento River within its banks and levees. California Governor Schwarzenegger declared a State of Emergency in February 2006 in an attempt to repair the levees, whose failure could impact the drinking water quality of two-thirds of California residents.