1. Was the knowledge that waters of different salinity, density and temperature do not mix unknown to anyone prior to Muhammad? Not really. A thousand years before Muhammad Aristotle wrote the following:
The drinkable, sweet water, then, is light and is all of it drawn up: the salt water is heavy and remains behind, Meteorology Book 2 Chapter 2
It is clear that at the time of Aristotle they knew that salt and fresh water don't immediately mix but that it takes time.
2. "Furthermore the separation of these waters are not permanent. The waters of various densities, salinities and temperatures eventually mix. The phenomenon is short lived and is observerabe only when the two bodies of water meet. It is like pouring milk in the cup of coffee. At first one can see that milk creates a current inside the coffee but eventually they mix."
http://www.faithfreedom.org/Articles/sina41003p4.htm
So congratulations Allah for mentioning in the Qu'ran something Aristotle knew a thousand years earlier, and congratulations Allah for explaining it so badly that Muslims still think that those seas never mix.