[15] This lack of riverwater begins in the 60 mi (97 km) between Friant Dam and Mendota,[16] where it is only replenished by the Delta-Mendota Canal (RM 205) and the Fresno Slough, when the Kings River is flooding.

[3] The majority of the river flows through quiet agricultural bottom lands, and as a result its meandering course manages to avoid most of the urban areas and cities in the San Joaquin Valley.

[17] The numerous tributaries of the San Joaquin – the Fresno, Chowchilla, Merced, Tuolumne, Mariposa Creek, Calaveras, Mokelumne, and others[18] – flowed freely across alluvial flood plains to join the river.

[26] The 268 mi (431 km) 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.

[26] The tremendous volume of sediments that underlie the lower San Joaquin River range from 6 to 9.5 mi (9.7 to 15.3 km) deep, with distance to bedrock generally increasing in a northerly direction.

[33] The rich vegetation and wildlife surrounding these bodies of water made the San Joaquin Valley a favored home as well as a stopping-off place for other nomadic peoples.

[35] 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.

Fages, accompanied by Father Juan Crespí, reached Mount Diablo near Suisun Bay on March 30 and there gazed upon the merging courses of the Sacramento, San Joaquin and Mokelumne Rivers.

[45][46] The San Joaquin River region remained largely unknown except for the fact of its existence until 1806, when Spanish explorer Gabriel Moraga led the first of several subsequent expeditions into the Central Valley, in order to find potential mission sites.

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".

[20] The city of Stockton, on the lower San Joaquin, quickly grew from a sleepy backwater to a thriving trading center, the stopping-off point for miners headed to the gold fields in the foothills of the Sierra.

[72] 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.

[74] 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.

[76] 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.

Two visionaries, railroad baron Henry E. Huntington and engineer John S. Eastwood established a fledgling power company in 1902 today known as Southern California Edison, and acquired water rights to the upper San Joaquin River from the Miller and Lux Corporation.

This is believed to be a result of the combination of the abrupt geometry change from the shallow river upstream of Stockton to the deep water channel, in addition to pollution from the harbor and city and poor tidal mixing.

In 1951, Mendota became the terminus of the Delta-Mendota Canal, a USBR project which conveys up to 4,600 cu ft/s (130 m3/s) for 117 mi (188 km) from the mouth of the Sacramento River to the usually dry San Joaquin at that point.

The passage of the Flood Control Act of 1944 included provisions for the construction of a levee system along part of the San Joaquin River, but valley farmers were not entirely satisfied.

After years of lobbying, farmers convinced the state government to authorize a massive flood-control system of diversion channels and levees whose main component is the Eastside Bypass, so named because of its location east of and parallel to the San Joaquin.

[108][109][110] Proponents of the project cite numerous benefits: flood control, increased storage, hydroelectric potential, and capacity to provide a greater flow in the downstream river during the dry season.

Today, this vegetation community exists only in isolated pockets because of development of the valley for agriculture, and in much of the remnant open areas where it once thrived, now grows introduced flora such as annual rye and wild oat.

[121] Human activities have replaced or altered over 95 percent of the historic wetlands as well as the California oak woodland habitat, which originally occurred along stream and river corridors in the foothills, and the tule grass that once thrived in huge stands on the edges of marshes and lakes.

[130] Initially, animals and plants thrived in the artificial wetlands that were created here, but in 1983, it was found that birds had suffered severe deformities and deaths due to steadily increasing levels of chemicals and toxins.

Also, with the introduction of better technology that allowed farmers to dig deeper wells and install electrical pumps, groundwater was seen as an often cheaper and easily accessible source compared to the river.

There has also been a lawsuit regarding damage to farmland west of the San Joaquin, near the town of Los Baños, claiming that the flows are seeping through levees that have not seen use in years due to the drying out of the river channel.

[150] In addition to the dry reaches, the higher discharge in the San Joaquin will help restore a total of 153 mi (246 km) of river, figuring in stretches with low or polluted flows.

Additional rehabilitation work is projected to continue until 2016 to ensure that the river can transport 4,500 cu ft/s (130 m3/s) of water through rainfall and releases from Friant Dam all the way to Bear Creek and the Eastside bypass.

[161] At 15,600 sq mi (40,000 km2), the San Joaquin River watershed proper drains a fair swath of inland central California, an area comparable to the size of the Upper Peninsula of Michigan.

[166] The main crop in the valley by annual sales is cotton, but more than 200 types of produce are grown along the San Joaquin River and in the Tulare Basin, including rice, almonds and lettuce.

[172] Land cover in the watershed is predominantly agriculture and forest, and large expanses of shrubland and semiarid foothill terrain also occupy portions of the basin in addition to a growing urban percentage.