Q. If the whole Earth was covered by water, where did Noah’s Flood waters go?
A. Yes, the whole earth was covered by water, including Mt Everest, at the time of the Flood. The Bible’s account is accurate and is supported by science and sometimes very simple explanations! Read the Scriptures we’ve listed at the end of this Answer; they will satisfy your enquiry and also inspire you to read God’s Word with holy awe!
Ps 104 tells how the mountains were covered with water, v6, and then God rebuked them and they fled, v7, the mountains rose, the valleys sank down, v8, and God set a boundary so that they will never again cover the Earth, v9. What a picture of God acting to alter the Earth’s topography. New continental landmasses bearing new mountain chains of folded rock strata were uplifted from below the globe-encircling waters that had eroded and levelled the pre-Flood topography. Large deep ocean basins were formed to receive and accommodate the Flood waters that then drained off the emerging continents.
That is why the oceans are so deep, and why there are folded mountain ranges.
If the Earth’s surface were levelled by smoothing out the topography of not only the land surface but also the rock surface on the ocean floor, the waters of the ocean would cover the Earth’s surface to a depth of 2.7km. Remember, nearly 70% of Earth’s surface is still covered by water. The waters of Noah’s Flood are in today’s ocean basins.
A comprehensive article is available upon request.