In "The Sky Tree" what existed in the beginning of time?

In Genesis chapter 1:2 God 's spirit was hovering over the surface of the waters." before God changed anything water existed on the Earth. In the sky tree it says that "In the beginning, earth was covered in water." so water had always been on Earth since the start.

Or ..? ⬇️

At an impressive 634 meters tall, the Tokyo Sky Tree's purpose is to act as a digital broadcaster, and although Dubai claims the title of the tallest man-made structure, the Burj Khalifa at 829 meters, Tokyo's new landmark holds the record for the tallest free-standing construction.