Indigenous people Archaeological finds near the southern end of the San Joaquin Valley suggested that humans first arrived in the region as early as 12,000 but no later than 5,000 years ago. In contrast, the Miwok occupied land deeper within the Sierra Nevada stretching north from the Merced River to the Mokelumne or the
American, a tributary of the Sacramento, and west to the Delta region. Most of the Miwok people in the watershed were part of the appropriately named
Sierra Miwok group. The Yokuts were unique among California natives in that they were divided into true tribes. Each had a name, a language, and a territory. Of the about 63 known Yokuts tribes, 33 lived along or around the San Joaquin River and its tributaries. The staple food for San Joaquin Valley inhabitants was the
acorn, which when ground, could be made into various foods such as cakes. Grinding the acorns was a simple process where they crushed the nuts using rocks in natural granite depressions. Many of the surviving examples of acorn milling areas can still be found in the foothills, especially around the
Kaweah River area. Another narrative does not mention Fages' name, but does say that Crespí was the one who reached Suisun Bay in 1772. During this visit, Crespí called the San Joaquin River "El Rio de San Francisco", a name that was not used widely due to the river's remoteness but persisted until the early 19th century. (background), where Juan Crespí first gazed upon the Sacramento-San Joaquin Delta in 1772, with Suisun Bay in the foreground In the autumn of 1772 Fages set out from
Mission San Luis Obispo de Tolosa in pursuit of deserters from the Spanish army, and traveled east then north over the
Tehachapi Mountains through
Tejón Pass, which today carries
Interstate 5 into the San Joaquin valley. After crossing the mountains, he came upon the shore of Buena Vista Lake at the southern end of the San Joaquin Valley, and gave the name
Buena Vista ("beautiful view") to the pass and a nearby Native American village. However, Fages did not venture farther north, and thus did not further explore the main stem of the San Joaquin River. California became part of
Mexico in 1821. The new government
secularized the Spanish missions and as a result the conversos in the missions were no longer protected by the missionaries from exploitation. The Mexican government began to tax the missions excessively. From 1820,
El Camino Viejo, a route between
Los Angeles and the San Francisco Bay along the west side of the San Joaquin Valley, brought settlements from the United States into the valley. During Mexican rule, the mission lands in the San Joaquin Valley were subdivided to wealthy landowners (
rancheros). The mission lands that were supposed to be given to the natives were also fraudulently taken over by American settlers. His expedition then turned east in an attempt to cross the Sierra Nevada. They tried to summit the range by way of both the Kings River and the
American River (a tributary of the Sacramento), but it was early spring and the snow was too deep. They crossed the mountains along the
Stanislaus River canyon, becoming the first recorded whites to cross the Sierra Nevada on foot. It is still disputed over whether Smith's party discovered
gold on the San Joaquin or one of its tributaries. Although some of his men confirmed it, Smith did not make any mention in his journal. In the early 1830s, a few fur trappers from the
Pacific Northwest exploring southwards into the San Joaquin Valley saw an epidemic of
smallpox and
malaria brought unintentionally by the Europeans that had swept down the San Joaquin River corridor during the summer of 1833, killing between 50 and 75 percent of the entire native population in the valley. The outbreak continued year after year with diminishing acuteness until about 50,000–60,000 indigenous people were dead. Explorer
Kit Carson noted in 1839 that "... cholera or some other fearful scourge broke out among them and raged with such fearful fatality that they were unable either to bury or burn their dead, and the air was filled with the stench of their decaying bodies." During the time Mexico was in control of California, the San Joaquin River region was only sparsely populated, and used almost exclusively for
cattle ranching. When California won
independence from Mexico in 1846, becoming part of the United States the following month, a flood of American settlers descended upon the valley. Just a year before,
Benjamin Davis Wilson "drove a herd of cattle from his Riverside rancho through the San Joaquin Valley to Stockton and reported seeing not a single white man". After the Americans took over, emigrants began trickling in increased numbers, establishing the towns of
Kingston City,
Millerton, and
Fresno City. The newcomers also included a group of
Mormons led by
Samuel Brannan, who sailed aboard the
Comet to establish a settlement at the confluence of the San Joaquin and the Stanislaus called "New Hope" (later
Stanislaus City). The real influx came in 1848, when a gold strike on the American set off the
California Gold Rush. Within one year, the population of the San Joaquin Valley increased by more than 80,000. quickly extended the length of the valley, some following old cattle routes and Native American trails, and were served by mule teams and covered wagons. Another notable but much smaller settlement was Las Juntas, near present-day
Mendota. This was a haven for criminals and fugitives, and was frequented by the infamous bandits
Joaquín Murrieta and
Tiburcio Vásquez. It was in the mid-1860s that the San Joaquin River and its surrounds underwent a substantial change: the introduction of irrigated agriculture. As early as 1863, small irrigation canals were built in the
Centerville area, southeast of Fresno, but were destroyed in subsequent floods. The vulnerability of the small local infrastructure led to the establishment of
irrigation districts, which were formed to construct and maintain canals in certain areas of the valley. One of the first was the Robla Canal Company in the Merced River area, which went into operation in March 1876, but was soon surpassed by the Farmers Canal Company. The district built a diversion dam on the Merced, sending its water into a pair of canals still in use today. Haggin soon ran into conflicts with other landowners over
riparian water rights, as the larger districts, including his, had more financial reserves and engineering expertise, and were the first to build dams and diversions on a large scale. This resulted in the drying out of streams and rivers before they reached downstream users and sparked conflict over how much water could be allotted to whom. In Haggin's case, his company ran into problems with the
Miller & Lux Corporation, run by
Henry Miller and
Charles Lux, who owned more than throughout the San Joaquin Valley, Tulare Basin, and other regions of California. The court battle that resulted would change water laws and rights in the San Joaquin River valley, and ended up promoting large-scale
agribusiness over small farmers. Miller and Lux were not any newer to the San Joaquin Valley than had been Haggin, but were the driving influence on valley agribusiness until well into the early 20th century. The corporation had begun acquiring land in the valley in 1858, eventually holding sway over an enormous swath reaching from the Kern River in the south to the Chowchilla River in the north. Much of the land that Miller and Lux acquired was swamp and marsh, which was considered virtually worthless. However, with their huge capital, they could afford to drain thousands of acres of it, beginning an enormous environmental change that eventually resulted in the loss of over 95 percent of the wetlands adjoining the San Joaquin River and Tulare Basin. Henry Miller exercised enormous political power in the state, and most San Joaquin Valley inhabitants either were avid supporters of him or despised him. When Miller died in 1916, his company owned in the San Joaquin Valley alone with hundreds of miles of well-developed, maintained irrigation canals. As said by Tom Mott, the son of Miller and Lux' irrigation superintendent, "Miller realized you couldn't do anything with the land unless you had the water to go with it. Perhaps more than any other person, Miller had more of a lasting impact on the San Joaquin River than any other individual." By the early 20th century, so much water was being diverted off the San Joaquin River and its tributaries that the river was no longer suitable for navigational purposes. As a result, commercial navigation began a decline starting in the late 19th century and was completely gone by 1911. With over under irrigation along the river by 1900 It has been said that fights over the river have caused "some of the most bitter and longest running lawsuits ever to clog the courts. Arguably, it is the most litigated river in America."{{cite news ==Dams, diversions and engineering==