the heavens and the earth came to exist ... long ago, by God's command

This can be stated in active form. AT: "God established the heavens and the earth ... long ago by his word" (See: rc://en/ta/man/translate/figs-activepassive)

came to exist out of water and through water

This means that God caused the land to come up out of the water, gathering the bodies of water together to make the land appear.