Yes, the game's engine will allow for different types of environments including underwater adventures.
Source: Official FAQ
Yes, there will be underwater adventure areas at launch. Ship travel is key to the game, and having something to do while sailing is therefore important. You can fight NPCs from your ship, and NPCs can pilot ships, so you can be attacked by, say, an NPC pirate. Also, there will be areas accessible only by ship and completely underwater. - 27 November 2005
Source: Aradune Mithara