Noahs Fish problem.
This is where the bible gets slightly cloudy It doesnt specify that noah took aboard fish, however he needed too, and it does say All animals. So we can assume he took aboard fish.
Especially since there are many fish that are sensitive to the salt content in the water, the flood would have lowered it and caused many fish to die. But since those fish are alive today, they must have been on board the ark. This posses an interesting problem for Noah. Not only did noah have to load all of those animals, he needed to find the correct salt and PH content water for these sensitive fish. He then needed to fill tanks for them and transfer the fish into those tanks. The bible lacks any description of how this activity was done.
Noah's Whale problem.
Im not quite sure, but I think some whales could have survived the Basics of the flood. However, if we look at the bible, god says he killed everything on earth (that wasnt on the ark). So we shall also assume this means all whales. Otherwise he really didnt kill everything.
Now, whales pose and interesting problem. Not only do they need water to swim in, but they need an air pocket to get oxygen from. This air pocket would need to be replenished with fresh oxygen, without filling up with water from the flood.
Just two blue whales alone would pose a big problem. If we go with an average size as 70 feet long, 16 feet wide and 16 feet tall. If you built a tank that the two whales could move in but was cramped. It would span the entire width of the ark at 81.25 feet. Around 145 feet long (only 5 feet longer than the two whales end to end). If the height of it was cramped and was only 25 feet high, only 9 feet of room to move, (this would limit the other two stories on noah ark (which was 48.75 feet tall) to 11.88 feet tall for each story). The tank would be 294,531.25 cubic feet of water or 2,203,246.75 Gallons of water. That would equal 9,363.8 Tons of water. For two animals. Not to mention the problem of getting the blue whales into the ark, as it was sealed before the flood waters came.
-Ari