There are way to many possible answers to this question.
First off, who said if there was a great flood that it would all be salt water? How would the fresh water fish survive?
I can explain how it wouldn't mix either.
Why couldn't there be worms in the ark?
Maybe these simple forms of life are indeed the only ones that evolve?
Maybe God created it that way.
I once saw a special about the ark, it said not only could it withstand the storms, where an oil tanker wouldn't, it had enough room on board to actually fit all the animals and supplies with a big space left over. After much though about what the extra space was for, it was then thought that the dinosaurs could have fit in the ark as well.