Then they show the above picture and comment: 

"There are large waves, strong currents, and tides in the Mediterranean Sea and the Atlantic Ocean. Mediterranean Sea water enters the Atlantic by Gibraltar. But their temperature, salinity, and densities do not change, because of the barrier that separates them."

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, people knew that waters of different density and salinity do not mix. 

The following picture is from the red sea. Obviously the sailors navigating in that sea must have noticed the difference of color between the waters. 

Also it seems that Muslims do not understand the phenomenon at all. The sill of Gibraltar, the barrier that separates the Atlantic from Mediterranean is not responsible for not letting the two waters to mix. The waters do not mix because of the difference in their density, salinity and temperature. 

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. 

Is Muhammad talking about the Waters of Atlantic and Mediterranean sea? No! There is no such mention in the Quran. It could be any two bodies of water. Was this phenomenon unknown to people at the time of Muhammad? No! This is quite an observable phenomenon. Anyone who has seen a delta where rivers carrying colored sediments enter the sea or where two rivers of different colors or two seas meet, can see that for a long distance the two waters keep apart. Muhammad had not been to many seas. But there is no reason to believe that he had not heard of this curious phenomenon from those who had been. The knowledge was known to all seamen and people loved to share the stories of their adventures. Therefore this verse is not a miracle. It is a casual statement of a curious phenomenon that he had heard and was impressed by it but without understanding the physics behind it. He thought it is the work of a deity called Allah that keeps the waters apart. 

As the verse 25:53 makes it clear, Muhammad is talking about two seas one with sweet and palatable and the other with salty and bitter water.

"And He it is Who hath given independence to the two seas (though they meet); one palatable, sweet, and the other saltish, bitter; and hath set a bar and a forbidding ban between them." [Pickthal translation]. 

 The water in both Atlantic and Mediterranean are salty. Therefore this verse does not refer to any two seas but to the waters at estuary where an arm of the sea extends inland to meet the river. In this case there is no “forbidding partitions” between the waters as Muhammad said and they eventually mix. On one side we have the fresh waters of the river running into the sea and on the other side we have the salty water of the sea being pushed away. In between the two we have a mixture of the two waters. The Islamic sites claim this water in between, acts as the barrier. This statement is simply asinine to say the least. The waters eventually keep mixing until all the salt water and sweet water become one. The mixed water between the two waters is not the barrier but the reverse. It is the mixture of the two.

One Muslim insisted that despite the fact that the phenomenon was known, at that time it is still a miracle because Muhammad was illiterate and he could not have known this and he insisted that I prove that Muhammad had heard this from someone. 

I find this quite absurd. If I write the theory of relativity and claim this is revealed to me and I never heard of Einstein, it is not up to you to prove I have heard of him. It is up to me to prove I have not.

Here what we did is prove that this knowledge existed prior to Muhammad. People knew that waters of different density do not mix and they could observer it. Despite that Muhammad assumes that the waters never mix. Which is obviously incorrect. De states that there is a barrier between the waters, which is of course untrue. These verses point to Muhammad’s ignorance and they are no miracles at all.