I don't have an issue with water - the ship survived the pressure of a black hole without even slightly buckling its pylons, water pressure is nothing by comparison. But actually, now that I think about it, two wrongs don't necessarily make a right... I suppose we have to assume that the structural integrity field holds the ship together at the limits of pressure.
I do however have an issue with a ship of that shape and size being able to take off and land on a planet though. They haven't set down on land - which would look very silly (although even by TMP, the saucer section was designed with the intention that it could detach and land). Surely the energy required to escape planetary gravity for something of that size and density is going to do a lot of damage to marine life? Massacreing plant and animal life for miles around isn't really Starfleet.