Okay, we already noted that Noah was going to have a very difficult time collecting the 13 million or so species of metazoans, especially from places such as the Pacific islands, the arctic, China, and indeed the vast majority of the planet which he didn't even know existed. And he probably would have had trouble telling apart the male and female beetles. But let's move on ...7 The Lord then said to Noah, “Go into the ark, you and your whole family, because I have found you righteous in this generation. 2 Take with you seven pairs of every kind of clean animal, a male and its mate, and one pair of every kind of unclean animal, a male and its mate, 3 and also seven pairs of every kind of bird, male and female, to keep their various kinds alive throughout the earth. 4 Seven days from now I will send rain on the earth for forty days and forty nights, and I will wipe from the face of the earth every living creature I have made.”5 And Noah did all that the Lord commanded him.
6 Noah was six hundred years old when the floodwaters came on the earth. 7 And Noah and his sons and his wife and his sons’ wives entered the ark to escape the waters of the flood. 8 Pairs of clean and unclean animals, of birds and of all creatures that move along the ground, 9 male and female, came to Noah and entered the ark, as God had commanded Noah. 10 And after the seven days the floodwaters came on the earth.
11 In the six hundredth year of Noah’s life, on the seventeenth day of the second month—on that day all the springs of the great deep burst forth, and the floodgates of the heavens were opened. 12 And rain fell on the earth forty days and forty nights.
13 On that very day Noah and his sons, Shem, Ham and Japheth, together with his wife and the wives of his three sons, entered the ark. 14 They had with them every wild animal according to its kind, all livestock according to their kinds, every creature that moves along the ground according to its kind and every bird according to its kind, everything with wings. 15 Pairs of all creatures that have the breath of life in them came to Noah and entered the ark. 16 The animals going in were male and female of every living thing, as God had commanded Noah. Then the Lord shut him in.
17 For forty days the flood kept coming on the earth, and as the waters increased they lifted the ark high above the earth. 18 The waters rose and increased greatly on the earth, and the ark floated on the surface of the water. 19 They rose greatly on the earth, and all the high mountains under the entire heavens were covered. 20 The waters rose and covered the mountains to a depth of more than fifteen cubits. 21 Every living thing that moved on land perished—birds, livestock, wild animals, all the creatures that swarm over the earth, and all mankind. 22 Everything on dry land that had the breath of life in its nostrils died. 23 Every living thing on the face of the earth was wiped out; people and animals and the creatures that move along the ground and the birds were wiped from the earth. Only Noah was left, and those with him in the ark.
24 The waters flooded the earth for a hundred and fifty days.
How does he know which animals are clean, and which are unclean? God doesn't reveal that information until Leviticus.
Remember Genesis 4? "4:20 And Adah bare Jabal: he was the father of such as dwell in tents, and of such as have cattle.4:21 And his brother's name was Jubal: he was the father of all such as handle the harp and organ.4:22 And Zillah, she also bare Tubalcain, an instructer of every artificer in brass and iron:" Well, after the flood there must not have been anybody who dwelled in tents and had cattle; or anybody who handled the harp and organ, because these are the descendants of Cain, whose line was exterminated in the flood. (Remember that Noah is a descendant of Seth.)
I don't think I need to go into the hydrology of the flood, but obviously, water flows downhill so it is impossible for a flood to cover all of the earth including the mountains. Floods can only occur locally in places where the water runs off more slowly than it accumulates. But leaving aside the impossibility of all this, why does God kill all the animals? What had they done to offend him? There's also the problem of the plants, which are not saved in the ark. Once the floodwaters are gone, what will the 30 million species of animals eat? On the other hand, God is happy with marine and aquatic creatures, which are evidently spared.
Did every living creature die in the flood. Apparently not, because as we will discover later, the Nephilim survived.
While one would have to be an utter fool to take any of this literally, the interesting question is what it might mean symbolically. Why is this story in the Bible? Why are we supposed to read it? What is it trying to tell us?