The muddy marsh/salt ponds surprised me too! But there are a few spots where the actual Bay (open water) is visible... e.g. Baylands Nature Preserve in Palo Alto. Also nearby hills have views -- I used to take walks to the top of the hill behind Google's Crittenden buildings, from where you can see a good bit of the southern Bay and up the peninsula northward. (Those hills also used to be MTV's garbage dump, so it could be worse!)