Good idea...
Not possible, 'm afraid.
Cause the water is a big block.
You can't just magically cut through it.
You can create physical zones in both the air and the water. Heck, you can even place water inside water in blockland. Water is a big physical block in the same way as the mission is, and multiple gravity/physical zones are possible.
Edit: Oh, and i wasnt talking about cutting the water. I mean creating a pocket of NotWater.