I know the devs have made an idea on this for a challenge mode, but i like the idea of having to make the player breed in water genes? Just like having to breed in cold resistance or stealth in the Long winter or 'Root of the problem' islands.
I very much like the idea of swimming and stuff, but as it stands, it's pretty boring. There are no threats or reason to even go down there. So before thinking about my idea i'd much prefer to get more diverse underwater ecosystems, but here's my idea anyway!
The island, upon arrival will receive rains in X amount of days, being detectable by your antennae bearing animals. After the time is up, heavy rains will begin to flood the island, sinking your helpless nichelings. Unless of course: they're in their element!
Perhaps you have to survive the flood as a gateway island? (Long island/Root jungle) Or maybe you start on small amount of land and have to cross a large amount of water to get to a new island.
(As for the predators, prey or plants, maybe they could be released with this island.)
Tell me what you think.