Question: Not clear on why God decided to kill the birds of the air and the creeping things on the earth. What did they do that grieved God? Then OK, He did destroy them in the flood, but I’m guessing that the fish of the seas were spared? They weren’t specifically mentioned. So was it that the fish of the seas where never really put under man’s control so, that’s why they were not destroyed?
Answer: God destroyed the whole earth and basically returned it to the state described in Genesis 1:2. It isn’t exactly clear why He chose this method which included man and animals but one good explanation is that He did this to wipe out mankind but the animal world was included because God had place the animal world under man’s authority/dominion. This includes the birds and the fish. Based on the fossil record lots of fish, perhaps most, died in the flood as well birds and land animals.
Question: If God destroyed the fishes in the water during the flood. Where did all the fish come from? Noah didn’t put them on the ark did he?
Answer: I believe you are correct that Noah didn’t put fish on the ark. God didn’t destroy all of them in the flood but many of them were destroyed and we know that because they ended up as fossils in rock layers on mountains. So, the fish we have today would have come from the fish that survived the flood.