Enough rain to flood the whole earth is a layer of fresh water over a mile thick... would the saltwater of the oceans be diluted to an extent that there would be mass extinction of several saltwater species? Or contrawise, wouldn't the brackish mix cause a problem for many freshwater species from the former lakes and rivers which have been subsumed within the advancing seas?
Worst case scenario is the ark needs both saltwater and freshater tanks for at least the most sensitive aquatic species. Then, doesn't Noah have to build some kind of mechanism to keep the water sufficiently oxygenated for 40 days and nights? Temperature regulation might be a problem, too.
Not to mention keeping the darned things clean. Yikes!
Man has always lived near water. The "whole earth" in that context meant the inhabited part; we are now living on areas which were viewed as plateaus prior to the flood and were sparsely if at all inhabited. The waters of the flood have not gone anywhere; there was simply not as much water on the Earth before the flood as there is now. As to salt, that apparently came with the flood. There is no reasonable theory as to a source of the salt in the oceans, on this planet at least.