Course
The river officially starts in the south-central Sierra Nevada at the confluence of two major affluents: the Middle Fork, arising out of Thousand Island Lake at almost 10,000 ft (3,000 m) above sea level; and the smaller North Fork, starting 1.8 mi (2.9 km) southeast of Mount Lyell. The Middle Fork is usually considered part of the main stem. From the mountainous alpine headwaters, the San Joaquin flows generally south into the foothills of the Sierra, passing through four hydroelectric dams. It eventually emerges from the foothills at what was once the town of Millerton, the location of Friant Dam since 1942, which forms Millerton Lake.
Below Friant Dam, the San Joaquin flows west-southwest out into the San Joaquin Valley – the southern part of the Great Central Valley – passing north of Fresno. With most of its water diverted into aqueducts, the river frequently runs dry in the 60 mi (97 km) between here and Mendota, where it is replenished by the Delta-Mendota Canal and intermittent flows from Fresno Slough, fed by the Kings River. From Mendota, the San Joaquin swings northwest, passing through many different channels, some natural and some man-made. Northeast of Dos Palos, it is joined by the Fresno and Chowchilla Rivers. Fifty miles (80 km) downstream, the Merced River empties into the San Joaquin.
The majority of the river flows through quiet agricultural bottomlands, and as a result its meandering course manages to avoid most of the urban areas and cities in the San Joaquin Valley. About 11 mi (18 km) west of Modesto, the San Joaquin meets its largest tributary, the Tuolumne. Near Vernalis, it is joined by another major tributary, the Stanislaus River. The river passes between Manteca and Tracy, where a pair of distributaries – the Old River and Middle River – split off from the main stem just above the Sacramento-San Joaquin Delta, a huge inverted river delta formed by sediment deposits of the Sacramento and San Joaquin Rivers.
About 40 mi (64 km) from the mouth, the river draws abreast to the western flank of Stockton, one of the basin's largest cities. From here to the mouth, the river is dredged as part of a navigation project, the Stockton Deep Water Ship Channel. Past the head of tide, amid the many islands of the delta, the San Joaquin is joined by two more tributaries: the Calaveras River and the larger Mokelumne. The river grows to almost 5,000 ft (1,500 m) wide before ending at its confluence with the Sacramento River, in Antioch, forming the head of Suisun Bay. The combined waters from the two rivers then flow west through the Carquinez Strait and San Francisco Bay into the Pacific.
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