In 1995, Anna Buising and
Jim Walker (B&W) reconstructed what the East Bay looked like over
the last 15 million years. To do this, they restored slip on faults,
removed tectonic distortions like squeezing or stretching, and identified
the parent-rock source of sandstones and conglomerates.
15 Ma (B&W Figure
3) 
- Most of Bay Area was
below sea level.
- The Pacific shoreline
trended WNW and lay well to the northeast of the modern bay.
- Rivers draining the
Sierran region brought sediment rich in pieces of volcanic rocks
that once must have lain atop the Sierran granites we currently
see. contained much of the volcanoes eroded from atop the Sierran
granites.
10 Ma (B&W Figure
4) 
- An oceanic embayment
invaded the East Bay, and accumulated shallow-marine and estuarine
sediment (small dot pattern).
- The Bay Block must have
been topographically high, for it contributed Franciscan sediment
eastward a low area in the "East Bay Hills Block" (EBHB).
5 Ma (B&W Figure
6) 
- The Livermore basin
(LB) became (and is) a low-lying area surrounded by hills.
- The Bay Block persisted
as a topographic high.
Why did areas rise and
fall?
Uplift and subsidence could be due to two causes:
- bends in right-lateral
strike-slip faults
Mt. Diablo, Santa Cruz Mtns and terraces, San Pablo Bay
- transpression (margin-wide)
(Coast Ranges)
Why did the Bay Block
change from a topographic high to SF Bay/Santa Clara Valley? 
No one knows for sure! Several models have been suggested, and are
summarized in the rather technical Figure 5 from Sedlock (1995).