A new fault map of the shelf offshore of San Francisco, California shows that faulting occurs as a distributed shear zone that involves many fault strands with the principal displacement taken up by the San Andreas fault and the eastern strand of the San Gregorio fault zone. Structures associated with the offshore faulting show compressive deformation near where the San Andreas fault goes offshore, but deformation becomes extensional several km to the north off of the Golden Gate. Our new fault map serves as the basis for a 3-D finite element model that shows that the block between the San Andreas and San Gregorio fault zone is subsiding at a long-term rate of about 0.2-0.3??mm/yr, with the maximum subsidence occurring northwest of the Golden Gate in the area of a mapped transtensional basin. Although the long-term rates of vertical displacement primarily show subsidence, the model of coseismic deformation associated with the 1906 San Francisco earthquake indicates that uplift on the order of 10-15??cm occurred in the block northeast of the San Andreas fault. Since 1906, 5-6??cm of regional subsidence has occurred in that block. One implication of our model is that the transfer of slip from the San Andreas fault to a fault 5??km to the east, the Golden Gate fault, is not required for the area offshore of San Francisco to be in extension. This has implications for both the deposition of thick Pliocene-Pleistocene sediments (the Merced Formation) observed east of the San Andreas fault, and the age of the Peninsula segment of the San Andreas fault.