It is impossible with Mission Editor. I believe this used to be possible before when Mission Editor came with Blockland, but it seems that ever since Space Guy's add-on has been required, the ability has been removed.
This is one of the biggest dilemmas I have found in map making, because it seriously restricts the amount of things you can do with water. Water must always be at the lowest point of your map.
Me and Boom were looking at the problem a few months ago, trying to find a loophole. However, he couldn't think of one that would be successful without having to go through a lot of extra trouble. The only legit possibility is just making the water from water bricks - although this is difficult because the water bricks cannot go underground or through interiors, and you must therefore align the map completely to the water. Then have the save file of the water bricks load on host spawn.