It's annoying trying to navmesh with the water there, so is there a way to hide it in the CK for a while?

From what I remember in the earlier games, water was the lowest level of a cell. To have dry land, the land was raised above the water (it could be lowered too)

So, try raising the land, doing what you need to do, then dropping it back.

Of course, none of this applies if you are making a pond or a bath or something similar. I think the water is keyed to the land level at that point.

Hit 1 twice to hide any selected object. Alt+1 unhides everything.