Even if Noah’s ark is scientifically possible with a bigger vessel that takes care of 8.7 million species, theologically it is not possible for God to handle a situation that puts greater hardship on the righteous than on the wicked who died in a few minutes after getting drown in the water.
However, if we look beneath the details, story tells God intervenes when it is necessary. God’s established practice is “Let the one who does wrong continue to do wrong; let the vile person continue to be vile.” (Revelation 22:11) This would mean that there is no intervention in the case of individuals and in each individual cases of free-will use; and it would also mean there would be a time when the righteous would find life is impossible because of the increasing number of the wicked (according to Law of increasing entropy). God, being the master of the universe, would need to act only on whole sale basis, hence would restore the original perfect condition, says logic (and also scriptures Rev 21:1, 5. Law of increasing entropy would again set things into a downhill trend, which would mean God would renew system of things again.
The above view takes care of the principle on which both theism and atheism stand: Theism says “From the more comes the less,” and atheism says “from the less comes the more.” Thus both agree that something comes from something. If something comes from something, it has always been true, it has always been there—infinite into the past and infinite into the future.