When swimming underwater the fly icon on creative will shown even if you are on survival or not, then while underwater and press down the fly icon button you will go more down and when reach it surface you will crouch but the crouch button is hidden and can't you able to go up and can't swim up, so wait for yourself to die before you can go up
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I think this is actually intended by the devs.

I think it's a new feature. When you are on water you can swim up and swim down without looking up to swim up or looking down to swim down. But the problem before is you can't go up when you reach surface but now it's fixed.
Still an issue in 1.6.0.1 - the flight controls appear and are functional some of the time underwater. The player no longer gets stuck in the sneak position underwater though.