Modern San Francisco Bay formed about 9,000 years ago, when glaciers melted from the last Ice Age, sea levels rose, and the ocean came in through the Golden Gate. Most of the sand and mud entering San Francisco Bay came through the Delta, and most of that came from the Sacramento River.
In the late 1800s, hydraulic gold mining in the Sierra Nevada dumped huge amounts of sand and mud into San Francisco Bay from the Sacramento River and San Joaquin River watersheds.
Sand and mud entered San Francisco Bay at 9 times the pre-Gold Rush rate. This created large new tidal flats and marshes.
In the 1900s, dams and flood controls reduced sand and mud entering San Francisco Bay. Dams trapped sand and mud, and reduced the peak river flows that transport most of the sand and mud. At the same time, levees, logging, urbanization, agriculture, and grazing, added sand and mud. Levees and landfills destroyed about 95% of the tidal marshes. The net result was reduced sand and mud entering San Francisco Bay, but still much more than before the Gold Rush.
Groundwater pumping in the Santa Clara Valley, especially from 1916 to 1966, caused the ground to sink up to 4 meters (13 feet), which caused widespread flooding of dry land near the South Bay. Reduced groundwater pumping after 1966 helped recover some of that land.
Since the early 1900s, dredging and aggregate mining have removed huge amounts of sand and mud from San Francisco Bay that are not being replaced.
Between 1957 and 2001, sand and mud from the Sacramento River dropped by half. The drop was caused by the end of hydraulic mining, dam construction, and water projects. The 1982-1983 El Niño floods permanently reduced sand and mud entering San Francisco Bay. By 1999, roughly equal amounts of sand and mud came from the Delta and local watersheds.
Since the 1960s, most of San Francisco Bay lost significant amounts of sand and mud. Erosion rates on the coast south of San Francisco have increased 50% since the 1980s. Mud suspended in the water dropped significantly between 1991 and 2007, which may have caused the collapse of several fish populations.
Timeline of major changes
Sediment transport in the San Francisco Bay Coastal System: an overview, Barnard, P.L., Schoellhamer, D.H., Jaffe, B.E., McKee, L.J., Marine Geology, 2013, https://doi.org/10.1016/j.margeo.2013.04.005
USGS Provides Long-Term Perspective for Integrated Science, USGS, https://sfbay.wr.usgs.gov/general_factsheets/integrated_science.html, accessed 5 December 2013.