Storm Wake by Lucy Christopher 

Moss has lived with her pa on a remote island for as long as she remembers. The Old World has disappeared beneath the waves - only Pa's magic, harnessing the wondrous stormflowers on the island, can save the sunken continents. But a storm is brewing, promising cataclysmic changes.

Soon, two strange boys wash up on the shore. As the clouds swell and the ocean churns, Moss learns to open her eyes to the truth about her isolated world ...