San Francisco Bay is unique on the California coast, a huge sheltered estuary with excellent harbors. (more below)
Photo (c) Andrew Alden, licensed to About.com
From front to back this view shows the ridge above Marin City, Belvedere island, Angel Island with its tassel of fog, the East Bay hills and Mount Diablo (click it to see full size). The islands were peninsulas during the ice ages, when the sea was 60 meters lower than today. At that time the San Joaquin River, draining all of central California, cut deep channels through today's bay area and through the Golden Gate. At the same time wide grasslands lined the coast, roamed by herds of mammoths and other large ice age mammals.
The East Bay hills are lifted up in connection with movement on the Hayward fault, part of the San Andreas fault system and America's most dangerous earthquake threat today.