even if you magically fit two of every species of animal in the world on any boat, much less one the size of noah's ark, they wouldn't survive after the flood. first of all, many of them live in colonies (e.g. ants), and couldn't survive if there were only two. most of the rest of the animals would be eaten or starve after they were removed from the boat. plus there's the ridiculous amount of food you'd need to carry to feed all of those animals for 40 days
the world was never really flooded like that
also, that kind of flood would certainly disturb sealife, so many sea animals would probably have died out as well