The Miwok Indians lived in the Central Valley among the delta's waterways, using them for food and transportation. The Yokut Indians also lived in the Northeast area of Stockton, along the Calaveras River up into the foothills following the South Fork of the river. The northern San Joaquin Valley was also the southern end of the Siskiyou Trail, a centuries-old footpath leading through the Sacramento Valley, over the Cascades, and onward to Oregon.

During the California Gold Rush, Stockton became a river port city, the hub of roads to the gold settlements in the San Joaquin Valley and northern terminus of the Stockton - Los Angeles Road. During its early years, Stockton was known by several names, including "Tuleburg", "Fat City," and "Mudville". Captain Weber decided on "Stockton" in honor of Commodore Robert F. Stockton. Stockton was the first community in California to have a name not of Spanish or Native American origin.

The city was officially incorporated on July 23, 1850, by the County Court, and the first city election was held on July 31, 1850. In 1851, the City of Stockton received its charter from the State of California. Early settlers included gold seekers from Asia, Africa, Australia, Europe, the Pacific Islands, Mexico and Canada. The historical population diversity is reflected in Stockton street names, architecture, numerous ethnic festivals, and in the faces and heritage of a majority of its citizens. In 1870, the Census Bureau reported Stockton's population as 87.6% white and 10.7% Asian