The San Francisco Bay is a region where the salt water of the Pacific Ocean mixes with the fresh water of the Sacramento (and San Joaquin) River.

The gap at the Golden Gate also allows the air over the Pacific Ocean to rush through the Golden Gate in the form of wind -- creating great opportunities for sailing! 

USGS & PG&E Portfolio of images of landscape, seascape and faults
of the San Francisco Bay area

The cartoonish diagram below is a little misleading since the average water depth in the bay is less than 20 feet (6 meters), the water depth in the south bay where we will be on the Discovery Voyage is only 11 to 14 feet deep.  At the Golden Gate, however, it is more than 300 feet deep (nearly 100 meters)  as 25 million gallons of water pass beneath the bridge each second when the tidal current is swift.

The land below the bay forms a stable block, which may be sinking very, very slowly.  

The cartoon at the right shows the mixing of the waters in the bay-- this region of mixing fresh and salt water is known as an estuary. Why would the salt water of the ocean (in green) shows flow below the fresh water from the rivers (in light blue) when mixing in the bay?