The Legend of Zelda - Spirit Tracks

From the introduction:

At the end of the Era of the Great Sea, a huge chunk of land that land been protected by barriers both sacred and dark suddenly lost those protections. As a result, a great deal of space that had been air was suddenly water. Disastrous for both those above and below, but in the long term it was a blessing. You see, as the water rushed in to fill that empty space, it meant that the level of the water above was lowering. In short, what had once been dry was now wet… and what was once wet was now dry.