I actually checked this out today to see if the water makes much of a difference on the frame-rate.

I went to the boat at Thanalan and tried looking straight at the water, what I noticed was the frame-rate sky-rocketed to a nice easy 60fps, lovely and smooth.

Then I spun the camera around to face away from the water and look up at the building, the moment the building came into view the frame-rate dropped down to 30-40 fps.

Then I looked back at the water and the frame-rate went back up, and slowly the boat started to move onto the camera from the right. The more of the boat came onto the screen, the lower the frame-rate went untill eventually it went down to the 30-40 fps I was getting from looking at the building.

I've also noticed the biggest spikes in frame-rate is caused from plants and bushes. So I don't think having water under the ground is actually the problem, I think it's how many polygons some parts of the enviroment are made from.

That's just what I think though.