[Ships and boats do have holes that do the same thing.](https://www.discoverboating.com/sites/default/files/what-is-a-bilge-pump.jpeg) Since there are places below the waterline where water can collect inside a ship’s hull a ship needs to be pumped out with a bilge pump rather than just draining out because of gravity like with a sit on top kayak.
Scuppers on kayaks work in exactly the same way as they do on ships. The top surface of the kayak, just like the weather deck on a ship, is above the water level. Still, water accumulates there due to splashes, waves, rain and for other reasons. But the deck is still above the water line so you can put scupper holes at the lowest level of the deck and the water will simply drain out. Ships’ weather decks slope slightly outward so the scuppers can simply be holes in the hull just at the level of that deck. Water can actually occasionally come back up through the scuppers onto the deck but it will just flow out again. Sometimes some kind of one-way-flow system or valve is used to limit the reverse flow.
The key is that both ships and kayaks have
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