is it possible to somehow do raycasting from underneath the boat and see then decide whether the water that covers the boat's area is to be rendered or not? Or is there some other much easier way or is it just impossible? we're supposed to be able to go down to a deck which is located underneath the watersurface.

Simple solution that wont work for all situations is to not render the water when you're inside the boat.

1. Render all geometry the usual way
2. Disable colour writes (but keep Z-writes)
3. Render a polygon sits on top of the boat like a cover
4. Re-enable colour writes
5. Render water