See this:

The transformation gizmos are fine, but icons, grid lines and others are rendered under the water. On stock Godot it's an annoyance at worst, however some addons I use render the information on the icon layer, meaning that important stuff is hidden under the water and I have to hide the water mesh just to see it.
//edit: Camera frustum preview is affected as well:

as well as the 3d path editor stuff:

So even with stock Godot the problem is bad.