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It's very strange, because I'm comparing this water to the water I saw in one of the campaigns. That water is just water; it looks like a normal body of water, but this water looks like a dug-out channel (you can see the ground beneath it; I can create a path along its bottom). Is this all that can be achieved in the editor?
There are three options (as far as I know):
a) Create a body of water with transparent water and a visible bottom;
b) Create a body of water with an invisible bottom (like a sea);
c) Place a crater on the map and fill it with water (the bottom is not visible, but it looks beautiful).
From your questions, it's not entirely clear what task you want to solve?