Now, that's a valid question!!
I have had no troubles at all flying over water. Many say to turn off VPS when doing so, but I haven't. I usually fly high when over water, so the VPS would have no bearing, but if you were flying low, say 50 feet or lower, it might.
We are in a coastal area so we fly over water all the time...no issues. For many, the pilot is just more nervous being over water, but the aircraft doesn't know the difference.