Yes, in Genesis, either God affected the earth a lot more than we think or a lot of it needs to be interpreted as metaphorical. Personally, I don't know which one to pick. Science doesn't seem to suggest any kind of global flood happening; there isn't enough water, so it may have been local. Or God, being God, made the water and then removed the water.
Fortunately, whether God exists affects the probability of this having actually happened, not the other way around, to an atheist pushing this point doesn't have too much of a base.