The Great Flood is one of the most monumental and traumatic events that have ever occured in Hyrulian history, which resulted in the complete inundation and destruction of the kingdom. The flood was a direct result of the invasion of Ganondorf following the Disappearance of the Hero, which saw the complete anihilation of Hyrulian armed forces during the conflict, leaving the kingdom completely unprotected from Ganondorf's wrath.

The people, realizing the hopelessness of their situation, prayed for the return of the Hero of Time, much like how Link first reappeared in Hyrule towards the end of the Imprisoning War and cast down Ganon's dark reign (or so the legend went). This time however, the Hero did not appear, and the people were left to their own devices. As a last effort, they directed their prayers to the Goddesses, hoping that the deities would somehow intervene on their behalf.

And so the Goddesses did, choosing to lock Hyrule away under a rising sea rather than let their chosen land fall to the dark machinations of the King of Evil. The Great Flood itself was never undone, only completed when King Daphnes Nohansen Hyrule chose to use the Triforce to finish the Goddesses' work and bring down the ocean completely on top of old Hyrule, thus destroying the kingdom forever.