I live on the coast, and my local testing ground is a park with a lake. I spend a LOT of time flying over water. The good thing about flying over water is there are no trees. Evil things, trees. Well, in a drone context
I have never had any doubt or worry about flying over water. The drone is always in line of sight, and the app will give you information about it's height above ground. I don't rely on the sensors and instruments, but what I can see by looking at the drone itself, and the footage coming back. I don't turn any of the sensors off when flying over water, and have never had any form of difficulty. If I'm going for a shot where the drone is low over the water (as I did in the week at an old watermill) I will always make sure I have a good view of the drone, and use my eyes to position it.
One thing you do have to understand is that the return to home point is set when you take off, and if you are on a moving boat, then it might decide to return (and land) on a part of the wet stuff where there is no longer a boat.