I'm having this same bug with scatterer (at least, I think it's scatterer, and it's with the atmosphere instead of the water). It's happening to me when the surface unloads (when I go above a certain altitude) while still in map view. When I go back to normal view the atmosphere, or in your case, the water, remains on the screen. Mine flickers.
To fix this, either do a scene change or make sure to be looking at your craft when you pass that altitude (about 150-250 kilometers).