'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.

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

In general, trees represent the deepest and most significant intellectual concepts: the ones that come to us most directly from the Lord. This varies depending on us and our states: the people of the Most Ancient Church, who were in a state of loving the Lord, understood truth automatically and internally through what the Writings call "perception"; people in lower states (including most of us) have to work a little harder to learn it from the Word and by willing to follow the Lord. In other parts of the Bible, especially in the prophets and New Testament parables, the meaning of "tree" is broader, meaning not just a person's intellectual concepts but the whole person.

'Trees,' as in Joel 1:10-12, signify knowledges.