The San Francisco Bay is a bay, estuary, and delta system that is approximately 3 to 12 miles wide by 48 to 60 miles long. Fed by the Sacramento, Napa, and San Joaquin Rivers, it drains into the Pacific Ocean from a small strait between San Francisco and Marin. It is spanned by numerous automobile bridges, including the Bay Bridge on the Eastern side of the peninsula, and the Golden Gate Bridge to the West. Additionally it can be traversed by ferry, or via BART in the trans-bay tube.

The Bay contains a number of islands including Alameda Island, Alcatraz, Angel Island, Red Rock Island, Treasure Island and Yerba Buena Island as well as several underwater rock formations.  As much of the Bay is only 12 to 15 feet deep, extensive shipping channels have been dredged to facilitate cargo freighters. The deepest point of the Bay, at 360 feet deep, lies underneath the Golden Gate Bridge

Originally ringed by salt marshes, tidal mudflats, and fresh water wetlands, the Bay has shrunk by up to a third as hydraulic mining and development have filled in the open bay and destroyed shoreline habitat. In the city of San Francisco; the Marina District, Downtown, Mission Bay, and portions of SOMA, the Mission, and Bayview Hunter's Point all sit on reclaimed wetlands.

The Bay ecosystem is also plagued by several invasive species - many originally introduced in ballast water at the Port of Oakland - including the Asian Clam, Atlantic Smooth Cordgrass, Chinese Mitten Crab, European Green Crab, Inland Silverside, and Water Hyancinth.