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The Delta is a complex network of channels and drained marshlands (islands) at the junction of the Sacramento River and San Joaquin River. Marshland draining caused the land to sink, so most of the islands are below sea level, some by as much as 4 meters (13 feet).
The Delta supplies more than 90% of the fresh water entering San Francisco Bay. Average flow from the Delta to the Bay is 800 cubic meters per second (211,000 gallons per second). The highest recorded flow is 17,800 cubic meters per second (4.7 million gallons per second). Huge pumps also send fresh water from the Delta south through canals, to the San Joaquin Valley and Southern California.
San Francisco Bay covers 1200 square kilometers (463 square miles) below sea level, and includes Suisun Bay, San Pablo Bay, Central San Francisco Bay, and South San Francisco Bay. Most sand and mud arrives in San Francisco Bay during the highest river flows, from late fall to early spring.
San Francisco Bay floor is mostly sand and mud over metamorphic and sedimentary bedrock. Bedrock can be found in Central Bay, the Golden Gate, the northern open coast, and Carquinez Strait. Mud covers most of South Bay and the shallower parts of Central Bay, San Pablo Bay, and Suisun Bay. Sand covers most of the open coast, Golden Gate, San Francisco Bar, and the deeper parts of Central Bay, San Pablo Bay, and Suisun Bay. Large sand waves and dunes are common in the main tidal channels.
Local winds create most of the waves in San Francisco Bay. Ocean swells through the Golden Gate affect exposed portions of Central Bay. Waves and ocean swells move a lot of sand and mud onto and off of shallow mudflats. The amount of sand and mud suspended in the water is highest in southern South Bay, moderate in Suisun and San Pablo Bays, and lowest in Central Bay. The amount of sand and mud suspended in the water is lowest during the summer and fall.
Today, local watersheds supply more than half of the sand and mud entering San Francisco Bay. Most of that comes in a few days, during and just after winter storms. High rainfall years might deliver four times as much as a low rainfall year.
The main path for sand movement is from the Sierra Nevada, through the Delta, Suisun Bay, San Pablo Bay, Central Bay, and Golden Gate, to the South Coast and offshore. Other paths include: northern Ocean Beach, through Baker Beach, to Crissy Field; offshore of Hunters Point, around San Francisco, to the Golden Gate and beyond; local rivers and creeks to South Bay and no farther; the Russian River south, around Point Reyes and offshore.
Every year, channel and harbor dredging removes roughly as much sand and mud from San Francisco Bay as comes in from the Delta. Mercury in hydraulic mining sand and mud continues to pollute San Francisco Bay.
Most of Suisun Bay is shallow and muddy, with several deeper sandy channels running east-west. Sand and mud suspended in the water are highest during winter freshwater flows from the Delta. During the spring and summer, onshore winds create waves that stir up sand and mud in both Suisun Bay and San Pablo Bay. Those waves can move sand and mud upstream from San Pablo Bay to Suisun Bay.
Salt water from the Pacific Ocean reaches Suisun Bay during the dry months only.
Carquinez Strait connects San Pablo Bay and Suisun Bay, and is 35 meters (115 feet) deep, and rocky. Peak tidal flows through Carquinez Strait are roughly 13,000 cubic meters per second (3.4 million gallons per second).
Most of San Pablo Bay is shallow and muddy. The main channel is 11 to 24 meters (36 to 79 feet) deep, and mostly sand. During high flows from the Delta, sand and mud takes several days to reach San Pablo Bay.
Salt water from the Pacific Ocean reaches San Pablo Bay all year.
Most of South Bay is shallow and muddy, and most of that mud comes from local watersheds. Strong winds during winter storms and summer sea breezes create waves, which stir up the mud. River flows into South Bay are much lower than into other parts of San Francisco Bay.
Central Bay is the deepest and sandiest part of San Francisco Bay, with the strongest currents. The western part has sand waves, sand dunes, and some exposed bedrock, while the eastern part is mostly muddy and flat. In parts of Central Bay, the sand and mud are 100 meters (328 feet) thick. Islands, bedrock, and sandbanks help create strong, rapidly changing currents, which create a wide range of shapes in the sand.
The Golden Gate is the narrow mouth of San Francisco Bay. The Golden Gate is bedrock underwater, with a maximum depth of 113 meters (370 feet). The depth and shape of the Golden Gate were created by a major earthquake fault, or by river erosion during the Ice Ages.
On average, tides move over 99% of the water going through the Golden Gate; less than 1% is fresh water. Golden Gate tides have a range of 1.78 m (5.8 feet), and tides can be measured all the way to the city of Sacramento.
Peak tidal flows through the Golden Gate are roughly 95,000 cubic meters per second (25 million gallons per second), traveling at over 2.5 meters per second (5.6 miles per hour). Sand and mud are transported through the Golden Gate by tidal flows and many other forces. Where the tidal flows slow down east and west of the Golden Gate, they deposit large areas of sand, including one of the largest sand wave fields in the world at San Francisco Bar.
San Francisco Bar is a large, sandy, underwater area just west of the Golden Gate, that covers roughly 175 square kilometers (68 square miles).
The open coast south of the Golden Gate is mostly sandy beaches and bluffs; to the north are rocky cliffs and pocket beaches. Large waves, strong tidal currents, and active earthquake faults create an extremely complicated system. Ocean swells create most waves and the largest waves. Strong northwesterly winds in the spring and summer create coastal upwelling and waves.
Ocean Beach in San Francisco builds up during the summer and fall, and erodes during winter storms, sometimes dramatically. South of Ocean Beach, erosion of coastal bluffs and landslides supply significant volumes of sand and mud from time to time. Erosion rates on the coast south of San Francisco are the highest in California.
Storm surges at the Golden Gate can raise sea level up to 70 centimeters (2.3 feet) temporarily. Storm surges can travel through the Golden Gate and San Francisco Bay, all the way to the Delta. During extreme storms, Suisun Bay can have even higher storm surges, because of increased river flows.
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