From its headwaters high in the Cuyamaca Mountains, the river flows generally southwest, first through rugged hinterlands but then into the urban areas surrounding its mouth at San Diego Bay.

[2] The Spanish called the river "Agua Dulce", a name they applied to good clear water anywhere they lived.

[3] The river rises as an intermittent trickle flowing out of Upper Green Valley, deep in the semi-arid Cuyamaca Mountains near Stonewall Peak.

As the river enters the Cleveland National Forest, it cuts through a steep and spectacular rocky gorge and crosses under a high bridge of Interstate 8.

[4] Continuing westwards, it receives the North Fork from the right, travels by the community of Rancho San Diego and passes through the Cottonwood Golf Club.

Bending northwest, the river enters a flood control channel and passes between National City and Chula Vista.

[8] In pre-American times, the Sweetwater River was a small but year-round stream, lined on both banks by extensive riparian forests, marshes and floodplains.

[12] The Spanish established settlements in the area in the 1760s mainly clustering around Mission San Diego de Alcala, calling the river Agua Dulce.

Later, after passing from the hands of Mexico to the United States, emigrants began arriving in the San Diego area in great numbers, many of them settling along the Sweetwater, establishing irrigated farms.

[13] By the late 1800s, the stream was described as having "practically no living water, except at its extreme sources and for 10 or 20 miles down from the summit of the range"[14] presumably because of the large irrigation diversions.

The first is Palo Verde Dam, a small rockfill structure about 2.5 miles (4.0 km) southeast of Alpine, serving mainly for recreation and flood control.

However, a report on the fauna of the county by Dr. David Hoffman in 1866 stated "Of the animal kingdom we have a fair variety: the grizzly bear, the antelope, the deer, the polecat, the beaver, the wildcat, the otter, the fox, the badger, the hare, the squirrel, and coyotes innumerable.

These parks have trails ranging along the east rim of a canyon, at the bottom of which runs the second San Diego aqueduct.

Commonly seen birds include the great egret, osprey, towhee, mallard, pintail, white-crowned sparrow and dowitcher.