Now first, I do realize that this does not affect the base ArmA 3 Alpha at this time, but it is something that would need to be addressed before the full game is out.

When opening up an island in ArmA 3 Alpha that has ponds (I am using Chernarus), it is currently impossible to swim on the surface of the water. Your character will enter the swim animation but will not move. It is possible to dive, however, and you can move about then.