I suppose it could be argued by a Creationist that the continents were lower at the time, and when the water came it flooded all over, and then the continents were raised. In that case, the water is still here.
In fact, that is precisely what some creationists DO argue. I call it the "Billiard Ball Earth Hypothesis". Basically, to cover the entire Earth with a minimum 15 cubits of water it is only necessary to assume that the maximum elevation to be covered was about the height of a smallish sand dune. Of course, I find it unlikely the ancient Hebrews were that ignorant. After all, the Mount Lebanon massif has a peak (Qornet es-Sauda) at around 3090m, and Mount Sinai/Jebel Musa runs about 2285m, both of which they knew about - so a literal flood in their eyes would have had to be at least 15 cubits higher than Qornet es-Sauda - which would tend to falsify the Billiard Ball Earth right there.