Gen. 1:1 states that God created the heavens and the earth. It then lists some of the features of that creation, like there were waters above "the firmament" and below, on the earth:

Gen 1:6-10
6 And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters.
7 And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so.
8 And God called the firmament Heaven. And the evening and the morning were the second day.
9 And God said, Let the waters under the heaven be gathered together unto one place, and let the dry land appear: and it was so.
10 And God called the dry land Earth; and the gathering together of the waters called he Seas: and God saw that it was good.

It is clear that there were waters above, and waters on the Earth called "Seas"

Later, in the 7th chapter, God caused the waters above to rain down on the earth, and caused water in the earth to gush up:

Gen 7:11-12
11 In the six hundredth year of Noah's life, in the second month, on the seventeenth day of the month, on the same day all the fountains of the great deep burst open, and the floodgates of the sky were opened.
12 And the rain fell upon the earth for forty days and forty nights.

This combination resulted in an end to the 1st heaven and earth. Peter explained it this way:

2 Pet 3:5-7
5 For this they willingly are ignorant of, that by the word of God the heavens were of old, and the earth standing out of the water and in the water:
6 Whereby the world that then was, being overflowed with water, perished:
7 But the heavens and the earth, which are now, by the same word are kept in store, reserved unto fire against the day of judgment and perdition of ungodly men.

In this context, the "world that then was" is not referring to a separate and different planet, but an age or civilization. It is clear, from the account in Scriptures, that Noah was in a boat, not a space craft. The ark came to rest on the same planet on which it was built. God destroyed that age, "Heaven and Earth", because of rampant sin. He will destroy this age, "The Second Heaven and Earth", for the same reason. This will NOT result in no Heaven or Earth! God inspired His prophets to write about a "New Heaven and Earth", and "The 3rd Heaven and Earth".