Short answer: They’re still here
Bible Text: Psalm 104:5-9
“Who laid the foundations of the earth, That it should not be moved for ever. Thou coveredst it with the deep as with a vesture; The waters stood above the mountains. At thy rebuke they fled; At the voice of thy thunder they hasted away (The mountains rose, the valleys sank down) Unto the place which thou hadst founded for them. Thou hast set a bound that they may not pass over; That they turn not again to cover the earth.”
Some folks object that if the great Flood covered all of the mountains as the Bible says, it would be impossibly deep – and where did all the water go?? This misconception arises from the idea that the great Flood covered the peaks of the world as they exist today. But Psalm 104 suggests that God altered the topography of the Earth. The creationist catastrophic plate tectonics model provides a mechanism for the rising of the mountains and the deepening of the ocean basins after the Flood.
As the new ocean floors cooled, they would have become denser and sunk, allowing water to flow off the continents. Movement of the water off the continents and into the oceans would have weighed down the ocean floor and lightened the continents, resulting in the further sinking of the ocean floor, as well as upward movement of the continents. The deepening of the ocean basins and the rising of the continents would have resulted in more water running off the land, carving out such landmarks as the Grand Canyon.
The collision of the tectonic plates would have pushed up mountain ranges also, especially toward the end of the flood, forming modern heights such as that of Everest. In other words, the current mountains ranges and ocean basins were created at the end of and after the Flood.
To be clear, the Bible says that the Flood waters covered the “high hills,” suggesting along with Psalm 104 that the topography of the pre-Flood Earth was less exaggerated. When you consider that if the Earth’s topography were leveled [above and below the oceans] the water would cover its surface by 1.7 miles, it’s not hard to see that the water is still here.