San Francisco Bay is a shallow, productive estuary through which water draining from approximately forty percent of California, flowing in the Sacramento and San Joaquin rivers from the Sierra Nevada mountains, enters the Pacific Ocean. Technically, both rivers flow into Suisun Bay, which flows through the Carquinez Strait to meet with the Napa River at the entrance to San Pablo Bay, which connects at its south end to San Francisco Bay, although the entire group of interconnected bays are often referred to as "San Francisco Bay."
The Bay covers somewhere between 400 and 1,600 square miles (1,040 to 4,160 square kilometres), depending on which sub-bays (such as San Pablo Bay), estuaries, wetlands, and so on are included in the measurement. The main part of the Bay measures 3 to 12 miles (5 to 20 km) wide east-to-west and somewhere between 1 and 2 north-to-south.
The bay was navigable as far south as San Jose until the 1850s, when hydraulic mining released massive amounts of sediment from the rivers that settled in those parts of the bay that had little or no current. Later, wetlands and inlets were deliberately filled in, reducing the Bay's size since the mid-1800s by as much as one third. Recently, large areas of wetlands have been restored, further confusing the issue of the Bay's size. Despite its value as a waterway and harbor, many thousands of acres of marshy wetlands forming the edges of the bay were considered for many years to be wasted space. As a result, soil excavated for building projects or dredged from channels was often dumped onto the wetlands and other parts of the bay as landfill. From the mid-1800s through the late 1900s, more than a third of the original bay was filled and often built on. The deep, damp soil in these areas is subject to liquefaction during earthquakes, and most of the major damage close to the Bay in the Loma Prieta earthquake of 1989 occurred to structures on these areas. The Marina District of San Francisco, hard hit by the 1989 earthquake, was built on fill that had been placed there for the Panama-Pacific International Exposition (1915), although liquefaction did not occur on a large scale. In the 1990s, San Francisco International Airport proposed filling in hundreds more acres to extend its overcrowded international runways in exchange for purchasing other parts of the bay and converting them back to wetlands. The idea was, and remains, controversial. (For further details, see the "Bay Fill and Depth Profile" section.)
There are four large islands in San Francisco Bay. Isolated in the center of the Bay is Alcatraz, the site of the famous federal penitentiary. Mountainous Yerba Buena Island is pierced by a tunnel linking the east and west spans of the San Francisco – Oakland Bay Bridge. Attached to the north is the artificial and flat Treasure Island, site of the 1939 Golden Gate International Exposition. Closest to shore, Angel Island was known as "Ellis Island West" because it served as the entry point for immigrants from East Asia. Raccoon Strait, between Tiburon and Angel Island, is the deepest part of the Bay. The federal prison on Alcatraz Island no longer functions, and the complex is now a popular tourist site.
The first recorded European discovery of San Francisco Bay was on November 4, 1769 when Spanish explorer Gaspar de Portolà, unable to find the port of Monterey, California, continued north close to what is now Pacifica and reached the summit of the high Sweeney Ridge, where he sighted San Francisco Bay.
The first European to enter the bay is believed to have been the Spanish explorer Juan de Ayala, who passed through the Golden Gate on August 5, 1775 in his ship the San Carlos, and moored in a bay of Angel Island now known as Ayala Cove.
This famous bay was the center of American settlement in the Far West during the 19th century. From the 1820s onward, American presidents and expansionists coveted the bay as a great natural harbor in the Pacific. After many failed efforts to buy the bay and varying areas around it, the US Navy and Army seized the region from Mexico during the Mexican-American War (1845-1848). On February 2, 1848 California was annexed to the U.S. with the signing of the Treaty of Guadalupe Hidalgo. A year and a half later, California requested to join the United States on December 3, 1849 and was accepted as the 31st State of the union on September 9, 1850. During the California gold rush of 1848-1850s, San Francisco Bay instantly became one of the world's greatest seaports, dominating shipping and transportation in the American West until the last years of the nineteenth century. The bay's regional importance became paramount when the transcontinental railroad reached its western terminus in Alameda on September 6, 1869 . The terminus was switched to the Oakland Long Wharf two months later on November 8, 1869.
San Francisco Bay continues to support some of the densest industrial production and urban settlement in the United States. The San Francisco Bay Area is the American West's second-largest urban area with approximately 8 million residents.
Tellingly, much of the SFBNWR consists of salt evaporation ponds purchased or leased from Leslie Salt Company and its successor, Cargill Corporation. These salt ponds produce salt for a variety of industrial purposes, including chlorine bleach and plastics manufacture, as well as supporting dense populations of brine shrimp, and therefore serving as feeding areas for waterfowl. In 2003, California and Cargill entered one of the largest private land purchases in American history, with the state and federal governments paying about $200 million for 16,000 acres (65 km²) of salt ponds in the south bay. SFBNWR and state biologists hope to restore some of the recently purchased ponds as tidal wetlands.
The seasonal range of water temperature in the Bay is from about 8 °C (46 °F) to about 23 °C (73 °F).
Humphrey the whale, entered San Francisco Bay twice on errant migrations, and was successfully rescued and redirected each time in the late 1980s and early 1990s. This occurred again with Dawn and Delta a mother a baby calf in 2007.
Industrial, mining, and other uses of mercury have resulted in a widespread distribution in the bay, with uptake in the bay's phytoplankton and contamination of its sportfish. In November 2007, a ship named Cosco Busan collided with the San Francisco – Oakland Bay Bridge and spilled over 58,000 gallons of bunker fuel, creating the largest oil spill in the region since 1996.
In the 1860s and continuing into the early twentieth century, miners dumped staggering quantities of mud and gravel from hydraulic mining operations into the upper Sacramento and San Joaquin Rivers. GK Gilbert's estimates of debris total more than eight times the amount of rock and dirt moved during construction of the Panama Canal. This material flowed down the rivers, progressively eroding into finer and finer sediment, until it reached the bay system. Here some of it settled, eventually filling in Suisun Bay, San Pablo Bay, and San Francisco Bay, in decreasing order of severity.
By the end of the nineteenth century, these "slickens" had filled in much of the shallow bay flats, raising the entire bay profile. New marshes were created in some areas.
In the last years of the nineteenth and first decades of the twentieth century, at the behest of local political officials and following Congressional orders, the US Army Corps began dredging the Sacramento and San Joaquin Rivers and the deep channels of San Francisco Bay. This work has continued without interruption ever since, an enormous federal subsidy of San Francisco Bay shipping. Some of the dredge spoils were initially dumped in the bay shallows (including helping to create "Treasure Island" on the former shoals to the north of Yerba Buena Island) and used to raise an island in the Sacramento-San Joaquin Delta. The net effect of dredging has been to maintain a narrow deep channel - deeper perhaps than the original bay channel - through a much shallower bay. At the same time, most of the marsh areas have been filled or blocked off from the bay by dikes.
San Francisco Bay is spanned by five bridges: the Golden Gate Bridge (which was the largest single span suspension bridge ever built at the time of its construction), the Richmond-San Rafael Bridge, the San Francisco – Oakland Bay Bridge, the Hayward-San Mateo Bridge, and the Dumbarton Bridge. The bay is also spanned by the Transbay Tube, an underwater tunnel through which BART runs. Prior to the construction of these infrastructures, transbay transportation was dominated by fleets of ferryboats operated by the Southern Pacific Railroad and the Key System transit company. However, in recent decades, ferries have returned, primarily serving commuters from Marin County, relieving the traffic bottleneck of the Golden Gate Bridge. (See article Ferries of San Francisco Bay).
The Bay also continues to serve as a major international shipping port, served by a large container facility operated by the Port of Oakland, and two smaller facilities in Richmond and San Francisco.