Great Flood

The is the name often associated with a deluge that befell the land of Hyrule many generations after the end of  in the Adult Timeline. Described in the introduction of, 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 generations 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. As the darkness was covering the land, the people of Hyrule prayed that the Hero of Time would once again come to save them, but the hero did not appear.

The Divine Deluge
The King of Hyrule, Daphnes Nohansen Hyrule, attempted to use his magic to stop Ganondorf, but failed. Left with no other choice, the people pleaded to the three Golden Goddesses. The Goddesses eventually answered the peoples' prayers, instructing those chosen to flee to Hyrule's mountaintops in order to escape the coming flood and to prevent Ganon's wish of the destruction of the land. Once the people were safely away, the Goddesses caused a torrential downpour, covering the land and turning the mountaintops into islands. The king chose to remain behind with his doomed kingdom. He split the Triforce of Wisdom into two parts and instructed the princess of that era to keep one piece and flee to the mountaintops with her servants.

Ganon's army had already infiltrated Hyrule Castle when 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 kingdom of color.

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.

Trivia

 * The Goddesses flooding the world to cleanse evil from the land, at the sacrifice of most life, while allowing a select few to survive, is similar to many flood myths from real life. Most notably, the Genesis flood narrative from the Hebrew bible, in which God sent a flood to cleanse sin from the Earth, and told the patriarch Noah to build an ark that would allow him, his family, and two of every kind of animal, to survive.