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So in my fantasy world, there exists a substance that -when applied to the surface of an object- repels water in the same way a very strong magnet would. This allows boats to hover above the surface of the water.

The people that use this substance are a small tropical island culture, and use their boats to hunt large creatures that can manipulate the water to defend themselves.

My question is this: what would be the optimal design for a boat that uses this substance in terms of balance, propulsion, and handling large waves? Assume pre-industrial technology, but any materials you’d like, since I haven’t nailed down that part of the world yet anyway.

Strangely enough, your boats aren't going to be THAT different from the boats we already have in terms of propulsion and wave handling. Balance is a completely different matter, but let's deal with each of these criteria one at a time.

Propulsion

You really have two options with your level of technology and they're the same options that everyone else had; oars and sails. Depending on how far above the water you sit though, oars are problematic because they have to be longer to get into the water meaning you need to be stronger to pull the oar. For open sea journeys this is an issue because putting the rowers close enough to the water to make oars effective is counter productive to being able to handle large waves, where you want high watertight 'walls' on the side of your boat (more on that later) so I'd stick with sails.

Sails could be managed by the people you describe technologically, especially as pre-industrial doesn't mean pre-science. There are plenty of examples in history of pre-industrial sailors who used sophisticated means to get their boats from one place to another in terms of both navigation and wind management so this is the best option. Just bear in mind, these kinds of large sailing vessels were a massive expenditure prior to industrialisation and they would be for your world as well.

Large Waves

Ultimately the best defence against high waves is high walls. On conventional ships, they sat very tall in the water (with massive ballast reserves in the hull to keep them upright) so as to survive high seas. Your floating boat will need the same walls, so your boat will still have a number of decks on it with walls on the side to stave off wave strike.

Balance (and Navigation because they're related)

These boats will have flat bottoms. It's that simple. You don't need to keep the boat from drifting in current because your boat floats above it in the first place, so there's no need for deep hulls. You MIGHT need keels though, because the sails are only part of the propulsion equation in that boats actually rely on some resistance against the hull to change direction. Rudders for instance need contact with the water to reorient the boat. So, your boat probably has a large rectangular square bottom to maximise the repulsion area against the water, hence maximising the balance of the boat. BUT, it also has a series of long keels that dip into the water (not coated with the repulsive material) that help with steering, and at least some of these will be on swivels that can be controlled from within the boat for steering. Ideally, these would be on the outer edges of the flat surface to preserve stability, like a catamaran.

So, your boat would look like a very large floating bathtub, with keels and sails below and above it respectively. That will allow it to balance, survive high seas, and move & navigate on the open sea.

Alright I think a flat hull will be by far the most stable design. You want a constant repelling force and a flat wide hull gives you stability against waves. At the same time you do want a somewhat high front against waves.

A

A tall front to steer against waves. This also gives you a vantage point to engage your prey with if they're large enough. Obviously this comes equipped with a railing, in fact your whole boat will be.

B

Back/front view. A wide flat hull for stability with a high railing on the main deck.

C

I was considering using your water repellent for some sort of ingenious propulsion mechanic before I realized you need to push that down in the water with more force then the boat weights. But maybe it will inspire you or someone else to make it work with some force multipliers.

D

An upgrade could be extra hulls not unlike a catamaran. The idea being you place those far and wide to give addition stability against waves from the sides. This will require some very strong water repellent to work. Extra strength by joining them with the mast against the central line of the ship.

E

Sails will be your best propulsion system. With no contact with water you should be able to get some frightening speeds.

Now for more specific details I turn you to regular ship design. You might want more storage space then a single space between your hull and the main deck. You probably want regular rudders in the back to aid with steering your vessel, regular rudders should work, uncoated. You might want multiple sails, again regular sources on sail design should have you covered.