It may be unassociated with the Bible, but the stories are similiar.
Bible: There were a bunch of non-believers/lazy people in the desert. God was really mad about this, and told Noah to build an arc, gather two of every animal (Male and Female), and wait. The others didn't believe him until their final destination came: He flooded the world. 40 days and 40 nights passed until the storms stopped. All the Nonbelievers had died in result of not believeing Noah. Noah sent out a bird to check on the status, and the bird brought sign of land. Then the earth eventually drained.
WindWaker: Ganon had the Triforce of Power and managed to break free from the Sacred Realm. The goddesses had come up with a final solution, to flood Hyrule, in order to save Hyrule. So, the goddesses told a few select people to go on the highest of mountains and wait for the storm to end. On Ganon's invasion of Hyrule Castle, the goddesses decided to flood Hyrule. Many people had died in the result of this, except for the believers that went up to the mountains. Only, the water didn't go down (Depending on what timeline you believe).
Simalarities were coated in Green.