In the beginning, God created the the heavens and the earth. The earth was without form and void, and darkness was over the face of the deep. And the Spirit of God was hovering over the face of the waters.
The heavens were made fully formed. There is no progressive shaping of heaven, but rather heaven is used as the pattern by which the earth is formed and filled and lighted. The Holy Spirit carries out the will of the Father in the creation to shape it according to the pattern of heaven, and in the fullness of time, to unite all things in Christ, things in heaven and things on earth.
The waters were divided into the earthly water, the water below the firmament, and the heavenly water, the water above. This is the water that the prophets see as a sea of glass or crystal before the throne of God. This is the water of blessing that comes down from above. Too much water, of course, means a flood, but even this is good. It cleanses the wicked out of the land so the land can flourish. Just as the earth was birthed out of water to become an abundantly fruitful and good creation, so are we birthed out of the water of baptism to be an abundantly fruitful new creation. And we are birthed from these heavenly waters.
John bore witness of Christ, saying, “this is he who baptizes with the Holy Spirit.” And Jesus later, talking with Nicodemus says, “Truly, truly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God. That which is born of the flesh is flesh, and that which is born of the Spirit is spirit.” So our baptism in the water and in the Spirit is our new birth. Again, the Spirit hovers over the face of the water and works the Father’s will. The Spirit fashions us after the pattern of heaven, Christ the new man. “Therefore, if anyone is in Christ, he is a new creation. The old has passed away; behold, the new has come.”