'Waters' particularly signify the spiritual parts of a person, or the intellectual aspects of faith, and also their opposites.

'The waters above the firmament,' as in Genesis 1:7, signify the knowledges in the internal self, and 'the waters beneath the firmament' signify the knowledges of the external self.

'Waters,' as in Ezekiel 47:9, refer to the New Jerusalem, and they signify spiritual things from a celestial origin.

'Many waters,' as in Revelation 17:1, signify truths of the Word adulterated. 'Waters' or 'rivers' signify spiritual, rational, or scientific things pertaining to truth.

'Waters … that go softly,' as in Isaiah 8:6-7, signify spiritual things, and 'waters … strong and many,' signify falsities.

'Waters,' as in Psalms 104:3, signify divine truths.

'Waters' signify truths in the natural self, and in the opposite sense, falsities.

'The waters were dried up from off the earth,' as in Genesis 8:7, signifies the apparent dissipation of falsities.

(Odkazy: Apocalypse Explained 17; Apocalypse Revealed 50; Genesis 8)

The number three in the Bible represents completeness. That's why Jesus rose on the third day after the Crucifixion -- his transformation was complete. It's why Elijah stretched himself on the dead child three times, why Jonah was in the belly of the fish for three days, why the Lord called Samuel three times, and many more. It's also reflected in the fact that there are three levels of heaven, three levels of hell, three levels to human life and, ultimately, three aspects of the Lord Himself: Father, Son and Holy Spirit.