Great Flood

The is the name often associated with a deluge that befell the land of Hyrule many years after the end of Ocarina of Time in the "Adult Timeline". Described in the introduction of The Wind Waker, it occurred when Ganondorf escaped from his imprisonment in the Sacred Realm and returned to Hyrule, after the departure of the Hero of Time.

Return of Ganondorf
Many years after the departure of the Hero of Time, the seal of the Seven Sages began to weaken for an unknown reason, and Ganondorf managed to escape his imprisonment. Ganondorf intended to make good on his threat to the Hero of Time and the Seven Sages that he would escape one day to make their descendants pay for his imprisonment. Ganondorf attacked Hyrule with his army. The King of Hyrule, Daphnes Nohansen Hyrule, attempted to use his magic to stop him, but failed, and left Hyrule's fate to the Goddesses. The people of Hyrule prayed that the Hero of Time would once again come to save them.

The Divine Deluge
The Hero of Time did not appear to save Hyrule, having been sent back across the flows of time to his own age. Left with no other choice, the people of Hyrule pleaded to the three Golden Goddesses. Ganondorf was on the verge of completely conquering the land of Hyrule, his troops having even penetrated Hyrule Castle itself. It was then however that the Goddesses answered the peoples' prayers, instructing them to flee to Hyrule's mountaintops in order to escape the coming flood. King Daphnes Nohansen Hyrule remained behind with his doomed kingdom, though evidenced by Tetra's survival, it is implied that he had Princess Zelda be among her people at the time of the flood. Once the people were safely away, the Goddesses caused a torrential downpour, covering the land and turning the mountaintops into islands.

The goddesses sealed the kingdom within an enchanted air chamber that prevented the water from destroying it. A magical seal was also cast over the Master Sword and the Pedestal of Time that froze the entire land of Hyrule and Ganon's army, freezing them in time and draining the entire castle of color. The Golden Goddesses then crafted a great tower that would serve to test the worthiness of any aspiring heroes, in an effort to find one capable of defeating Ganon. Only one who passed tower's trials would be sent beneath the waves to Hyrule Castle deep to take the up the Master Sword. This tower could only be raised from the bottom of the sea by one possessing the three special Pearls of the Goddesses, one for each Goddess.

The people of Hyrule would then go on to build a new civilization on the surface of the Great Sea and, with the passing of time, largely forget the memory of the old Hyrule that still existed deep beneath the waves.

Aftermath
Many centuries after the initial flood, Ganondorf broke free of the seal binding Hyrule and returned, intending to reunite the Triforce pieces to reconquer the sunken Hyrule. This caused a new incarnation of Link and Princess Zelda to appear to challenge Ganondorf again, as had their predecessors. After uniting the Triforce, and at the will of the old King, the sacred pieces rise into the air and vanish as the air chamber above them begins to collapse, allowing the Great Sea to pour into Hyrule. After Ganondorf is defeated, Hyrule is completely swallowed by water, leaving Link and Princess Zelda to create a new Hyrule above the waves.