Prior to incorporation in 1850, the area now encompassing San Joaquin County was inhabited by the Yokuts and Miwok native peoples.

These communities lived in villages throughout the region, consuming diverse diets that reflected the flora and fauna of the California Delta.

Between 1843 and 1846, during the era when California was a province of independent Mexico, five Mexican land grants were made in what would become San Joaquin County: Rancho Campo de los Franceses, Pescadero (Grimes), Pescadero (Pico), Sanjon de los Moquelumnes, and Thompson.

The largest of these grants was the Rancho Campos de los Franceses, secured by Charles Weber and Guillermo Gulnac, which was eventually developed into the city of Stockton.

As the Gold Rush drew miners to the Sierra Nevada, Stockton grew into a major logistical and mercantile hub for the San Joaquin Valley and mother lode, which allowed for the City and County populations to rise significantly between 1850 and 1870.

As the state's gold economy waned in the 1870s, San Joaquin County transitioned into a major national center of agriculture, which it remains to this day.

The importance of agriculture to the region's economy led to the creation of a dynamic industrial engineering sector in Stockton, Lodi, and nearby Rio Vista in the 1880s.

In the early 1900s, the Santa Fe Railroad constructed from Bakersfield and Fresno went through Stockton to travel northwards, reaching Oakland.

Smaller lines constructed at Stockton were the Tidewater Southern to Modesto and the Central California Traction to Sacramento.

[15] The county has a very low inland elevation and a very flat drainage basin for the San Joaquin River and its numerous tributaries.

With the resulting exceptionally high water table, the county is a marshy and swampy delta with a tendency to flood in the spring with melting snow runoff from the Sierra Nevada Mountains.

The United States Office of Management and Budget has designated San Joaquin County as the Stockton–Lodi, CA Metropolitan Statistical Area.

[40] Some chartered cities such as Stockton and Tracy provide their own municipal services such as police, public safety, libraries, parks and recreation, and zoning.

Municipalities within the county that have municipal police departments are: Stockton, 310,000; Tracy, 89,000; Manteca, 77,000; Lodi, 65,000; Lathrop, 23,000 (sheriff contract); Ripon, 17,000; Escalon, 7,200, In the United States House of Representatives, San Joaquin County is split between California's 9th and 13th congressional districts,[50] represented by Josh Harder (D–Tracy) and Adam Gray (D–Merced), respectively.

[53] On November 4, 2008, San Joaquin County voted 65.5% in favor of Proposition 8 which amended the California Constitution to ban same-sex marriages.

In 2016, Hillary Clinton became the first Democratic nominee who lost nationally to win the county, and she did so by a sizable margin of around 14 points.

Conversely, Donald Trump posted the worst result in county history for a national Republican Electoral College winner, being held to under 40% of the vote.

Number of incidents reported and crime rate per 1,000 persons for each type: As of 2018, the gross value of agricultural production in the county was $2.6 billion.

[59] San Joaquin County is home to one of the largest walnut processing facilities in the world, DeRuosi Nut.

Another large company, Pacific State Bancorp (PSBC), was based there but was closed by the California Department of Financial Institutions on August 20, 2010.

[62] As of 2013, the goods movement industry is also an important part of the local economy, with an Amazon fulfillment center in Tracy and the Port of Stockton.

Artifact is a San Joaquin Delta College periodical based in Stockton since December 2006, featuring writing in all genres, photography, and visual media by students, staff and faculty as well as community members.

The television show Sons of Anarchy was set in Charming, California, a fictional town in San Joaquin County.

RTD Hopper is a public bus service operated by San Joaquin Regional Transit connecting Stockton to Ripon, Manteca, Tracy, Lodi, and Lathrop.