Hey Kim! I'm not from the Bay area, so i may not have very useful information, but here are some quick thoughts:

1. Best thing probably is to get in touch with whatever is the local chapter of the National Speleological Society: www.caves.org/ Also, the San Francisco grotto is at www.caves.org/grotto/sfbc/ They ought to be enthused to have you involved.

2. Cave conservation tends to be a BIG problem and is taken very seriously by the caving community. Over the years a great deal of irreparable damage has been done to the cave environment and to cave formations by careless `tourist' type `spelunkers'. What this means is that the serious caving community has developed a little along the lines of a terrorist organization :-) In other words, there are local `cells' or grottoes that often are very tight-lipped about where the caves are and how to visit them until you have been a round a little bit, maybe gone on some easy trips with people and shown that you can be a mature, responsible caver. That's why if you want to go to the interesting caves, you almost certainly want to get involved with a local grotto. On the face of it, it kinda sucks, but once you actually meet the people in the grottoes you will probably be happy you did, since they are usually really nice people.

3. I don't know about any submerged caves in the Bay area. Haven't heard of any, but that doesn't mean they aren't there. But cave diving is a whole 'nother beast. If you haven't taken an open water course yet, i can tell you now that what they'll tell you about cave diving is that it is really really dangerous and not to even think about diving a cave unless you have done all the cave training first, and they aren't likely to even let you start cave diving training until you've got at least a good 100 dives under your belt. There are a LOT of gotchas in cave diving that really can kill you quick. Not trying to discourage you, just letting you know that working and gearing up to do cave diving safely is a pretty serious undertaking. Some places to look into it are:

www.nsscds.com/
www.safecavediving.com/
www.cavediver.net/

Hope some of that is helpful.