Does the MSQ contain underwater parts?

[MitsukiKimura]

Odd question, but does the MSQ ever require you to go umderwater?

Some quick searching informed me that there are underwater areas, but since I am trying to avoid storyline spoilers I can't confirm if these areas are just optional/side-quest areas or part of the MSQ.

Much like the person in the below post, my wife is absolutely terrified of sharks and WILL NOT go underwater (even in a game).
http://forum.square-enix.com/ffxiv/threads/332438

I believe there is a part in Stormblood where you have to go underwater to unlock one of its dungeons. Rather not spoil the dungeon name o/