The San Joaquin River ( ; ) is the longest river of Central California. The long river starts in the high Sierra Nevada and flows through the rich agricultural region of the northern San Joaquin Valley before reaching Suisun Bay, San Francisco Bay, and the Pacific Ocean. An important source of irrigation water as well as a wildlife corridor, the San Joaquin is among the most heavily dammed and diverted of California's rivers.
People have inhabited the San Joaquin Valley for more than 8,000 years, and it was one of the major population centers of pre-Columbian California. Starting in the late 18th century, successive waves of explorers then settlers, mainly Spanish and American, emigrated to the San Joaquin basin. When Spain colonized the area, they sent soldiers from Mexico, who were usually of mixed native Mexican and Spanish birth, led by Spanish officers. Franciscan missionaries from Spain came with expeditions to evangelize the natives by teaching them about the Catholic faith.
Once an inland sea, most of the San Joaquin Valley has a very uniform topography, and much of the lower river formed a huge flood basin. In the 20th century, many levees and dams were built on the San Joaquin and all of its major tributaries. These engineering works changed the fluctuating nature of the river forever and cut off the Tulare Basin from the rest of the San Joaquin watershed. Once a habitat for hundreds of thousands of spawning salmon and millions of migratory birds, today the river is subject to tremendous water supply, navigation, and regulation works by various federal agencies, which have dramatically reduced the flow of the river since the 20th century.
Name
The river was called many different names; at times different parts of the river were known by different names. The southern Yokuts called the river, Tihshachu (Tih-shah-choo), meaning salmon-spearing place. The present name of the river dates to 1805–1808, when Spanish explorer Gabriel Moraga was surveying east from Mission San José in order to find possible sites for a mission. Moraga named a tributary of the river (it is not known which one) for Saint Joachim, husband of Saint Anne and father of Mary, the mother of Jesus. The name Moraga chose was later applied to the entire river; it was in common use by 1810.
In 1827, Jedediah Smith wrote in his journal that an unknown group of Native Americans called the river the Peticutry, a name which is listed as a variant in the U.S. Geological Survey (USGS) Geographic Names Information System.
An earlier name for the lower section of the San Joaquin was Rio de San Francisco, which was the name Father Juan Crespí gave to the river he could see entering the Sacramento-San Joaquin Delta from the south. A member of the Pedro Fages party in 1772, Crespi's vantage point was the hilltops behind modern Antioch. Another early name was Rio San Juan Bautista, the origin of which is unknown.
Course
thumb|Crossings of [[California State Route 99 and the Union Pacific Railroad along the northern border of Fresno. The early stages of construction of California High-Speed Rail's San Joaquin River Viaduct is also visible.]]
thumb|The San Joaquin at [[Mendota Pool during the high flows of April 2006]]
The river's source is located in the Ansel Adams Wilderness, in the south-central Sierra Nevada at the confluence of three major affluents: the Middle Fork, which rises from Thousand Island Lake at almost above sea level, and the South Fork, which begins at Martha Lake in Kings Canyon National Park and flows through Florence Lake, joins a short distance downstream. The Middle Fork is considered the largest of the 3 forks. 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 (RM267), 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 a 150-mile section. This lack of riverwater begins in the between Friant Dam and Mendota, where it is only replenished by the Delta-Mendota Canal (RM 205) and the Fresno Slough, when the Kings River is flooding. From Mendota, the San Joaquin swings northwest, passing through many different channels, some natural and some man-made. Northeast of Dos Palos, it is only joined by the Fresno and Chowchilla Rivers when they reach flood stage. downstream, the Merced River empties into an otherwise dry San Joaquin (RM118). The numerous tributaries of the San Joaquin – the Fresno, Chowchilla, Merced, Tuolumne, Mariposa Creek, Calaveras, Mokelumne, and others – flowed freely across alluvial flood plains to join the river. All of the major tributaries of the river originate in the Sierra Nevada; most of the streams that start in the Coast Range are intermittent, and contribute little to the flow of the San Joaquin. During the winter, spring, and early summer, storms and snowmelt swell the river; in 1914 – before the development of major dams and irrigation diversions – the California Department of Engineering estimated the river's flow in full flood at . This range is less extreme than the temperatures below Vernalis where the range is from 2°Celsius (35.6 °F)on Dec 26, 1987 to on August 9, 1990. The river typically ends above the Mendota Pool. Larger flows in the fall may make it possible for the river to extend further towards the ocean, but for the last several years, this is a rare occurrence. The water is largely held behind Friant Dam.
The typical monthly flow of the San Joaquin River near the Sack Dam is 0. There have been seepage concerns below this part of the river, so current flows are restricted below the Sack Dam.
The present annual flow of the San Joaquin River near Vernalis is about , or 4.5 million acre-feet (5.6 million m<sup>3</sup>) per year. According to USGS stream gauge #11303500 at Vernalis, above Suisun Bay and below the mouth of the Stanislaus River, the average discharge of the San Joaquin River between 1924 and 2011 was , or 3.3 million acre-feet (4.0 million m<sup>3</sup>) per year. The highest recorded annual mean was , 15.4 million acre-feet (19.0 million m<sup>3</sup>), in 1983, while the lowest was , , in 1977.<br>
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Geology
thumb|left|Headwaters of the Middle Fork San Joaquin River, just downstream of [[Thousand Island Lake]]
In a geologic context, the San Joaquin River can be divided into two major segments. The upper above Friant Dam in the Sierra is characterized as a steep-gradient, rocky mountain stream. Over millions of years, the upper San Joaquin, as well as the upper reaches of most of its tributaries, have eroded enormous amounts of rock and sediment from the mountains. Most of the Sierras are underlain by granitic igneous and metamorphic rock dating back to the Mesozoic Era (250–66 MYA); in addition many of the San Joaquin's tributaries flow across a foothills region of metamorphosed volcanic rock more famously known as the Mother Lode Gold Belt.
The lower part of the river, in sharp contrast, is a meandering stream flowing over Cenozoic alluvial deposits (66 MYA-present), which together comprise the flat floor of the Central Valley. Compressional forces along the boundary of the North American and Pacific Plates between 2–4 MYA resulted in the uplift of the Coast Ranges, creating an enclosed basin today known as the Central Valley and resulted in the San Joaquin's present path to the sea.
Because of its highly permeable nature, the San Joaquin River's valley is underlain by one of the largest aquifers in the Western United States. The aquifer underlying the San Joaquin River and Tulare Basin is estimated to hold nearly of water, of which about half can be pumped economically or is clean enough for human use.