Short answer
The Qur'an says that God (﷾) lets two bodies of water meet, and sets a barrier between them, so that neither overruns the other. In one verse the two are fresh and salt water. Where a large river such as the Mississippi meets the sea, the fresh water rides over the salt for a long way. In another verse two seas meet. At the Strait of Gibraltar the salty Mediterranean runs out beneath the Atlantic. It flows on at depth for hundreds of kilometres, still separate. It mixes at first, yet it stays saltier than the water around it, so each sea keeps its own character. No one could see this from the surface, and instruments first measured it in modern times. The Qur'an was revealed to the Prophet (ﷺ), who is not known ever to have sailed. The Qur'an counts this barrier among God's (﷾) signs.
Full explanation
What the Qur'an says
The Qur'an names a barzakh (a barrier) between two waters. In 25:53 one is sweet and one is salt, and the barrier is "a partition that is forbidden to be passed". In 55:19-20 two seas meet, and "they do not transgress" the barrier between them. Elsewhere the Qur'an counts this separating bar among the signs that there is no god besides Allah (﷾).
“It is He Who has let free the two bodies of flowing water: One palatable and sweet, and the other salt and bitter; yet has He made a barrier between them, a partition that is forbidden to be passed.”
“He has let free the two bodies of flowing water, meeting together: Between them is a Barrier which they do not transgress:”
“Or, Who has made the earth firm to live in; made rivers in its midst; set thereon mountains immovable; and made a separating bar between the two bodies of flowing water? (can there be another) god besides Allah? Nay, most of them know not.”
Where a river meets the sea
Where a strong river runs into the sea, the lighter fresh water spreads over the heavier salt water. Between them lies a zone where the saltiness changes quickly. The two waters can stay apart for a long distance. A fisherman in an estuary (the wide mouth of a river) knows this. It is not offered as a discovery. It is one more statement in the Qur'an that is accurate.
“It is He Who has let free the two bodies of flowing water: One palatable and sweet, and the other salt and bitter; yet has He made a barrier between them, a partition that is forbidden to be passed.”
Explains that river water entering an estuary is less salty and less dense than sea water, so it often floats on top of it; in a salt-wedge estuary a sharp boundary forms, with fresh water above and a wedge of salt water below.
The Strait of Gibraltar
At Gibraltar the salty Mediterranean meets the fresher Atlantic. Atlantic water flows in on top. Mediterranean water pours out beneath it, over the ridge of the strait. At first it mixes strongly with Atlantic water. Yet it stays saltier than the water around it, and it goes on westward. It settles at around 1,000 metres, a separate body of water that oceanographers (scientists who study the sea) trace across the Atlantic. Scientists first measured it with instruments in the nineteenth century, and mapped it in detail in the twentieth.
Measures the salty, dense water that pours out of the Mediterranean through the Strait of Gibraltar. It mixes strongly with Atlantic water as it first runs down the slope west of the strait, then flows on westward and settles inside the Atlantic, where it remains an important, distinct body of water.
Why this is a sign
The Qur'an was revealed to the Prophet (ﷺ) in Mecca. Mecca is more than 4,000 kilometres from Gibraltar, and the Prophet (ﷺ) is not recorded as ever having sailed. A caravan merchant going to Syria saw no strait at all. The boundary under the sea cannot be seen from the surface, and no one he could have met had measured it. Yet the Qur'an says the two seas meet, that a barrier lies between them, and that each stays distinct where they meet. The Qur'an itself says God (﷾) will show His signs until it is clear that it is the truth.
“He has let free the two bodies of flowing water, meeting together: Between them is a Barrier which they do not transgress:”
Measures the salty, dense water that pours out of the Mediterranean through the Strait of Gibraltar. It mixes strongly with Atlantic water as it first runs down the slope west of the strait, then flows on westward and settles inside the Atlantic, where it remains an important, distinct body of water.
“Soon will We show them our Signs in the (furthest) regions (of the earth), and in their own souls, until it becomes manifest to them that this is the Truth. Is it not enough that thy Lord doth witness all things?”
Perspectives
The Islamic perspective
The Qur'an, revealed to the Prophet (ﷺ), describes waters that meet but stay distinct. This is true where large rivers meet the sea, and where seas meet each other. It is a sign that the Qur'an is from God (﷾).
The Qur'an says God (﷾) set a barrier between sweet and salt water. He also set one between two seas that meet, which they do not pass.
In many estuaries, fresh river water lies over salt sea water with a zone of changing saltiness between them.
Mediterranean water leaves through the Strait of Gibraltar beneath the Atlantic. It spreads into the Atlantic as a distinct body of water.
The boundary where the two seas meet and stay distinct could not be seen or measured in the seventh century. So the Qur'an's accurate description is a sign.
The Qur'an presents the separating barrier as a sign of the one God (﷾).