What did animals that require large populations to survive do? For exmple, one male and female bee, ant, termite and mole rat cannot survive as a single pair. I imagine several of the pack hunting species would have difficulty too... e.g. lions and wolves.
How did penguins get from Mt Ararat to Antarctica?
And the massive inundation of Fresh water would kill all the marine fish. Alternatively, if the incoming water was saline, it would kill all the fresh water fish.
Post flood, when water levels return to normal, the decaying carcasses of 99.99% of the biosphere would cause serious problems in terms of water quality, putrescence and general environmental degredation.
terestrial vegetation can't survive long fully immersed, 40 days submergeance would kill all land dwelling species of plant. Marine vegetation is usually closely adapted to its depth, i.e. a sudden change either deeper or shallower will kill most aquatic plants. Not so much a problem for free floating species, but the various species of rooted aquatic plant, like seawood and kelp, would be wiped out by being plunged under presumeably hundreds, if not thousands, of metres of water. So then, even when Noah lets all the animals out of the Ark, all the highly specialised animals who live in rain forrests, or grasslands environments, or in kelp forrests, are going to have some serious problems.
Of course, God could miraculously mirical all these problems away, but it seems kind of unlikely that the bible doesn't mention this.