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A barrier between two seas
When a fresh water river flows into the sea or ocean, there is a transition region in between. This transition region is called an estuary where the fresh water remains temporarily separated from the salt water. However, this separation is not absolute, is not permanent, and the different salinity levels between the two bodies of water eventually homogenize. The Qur'an, by contrast, suggests that there is a separation between two seas, one salty and one fresh water, maintained by some sort of divine barrier placed between them.
Furthemore, Quran 55:20 quoted below states that coral emerge from both seas. However, coral are found only in salt water oceans, and exposure to freshwater leads to coral bleaching.
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.
Quran 25:53
Is He [not best] who made the earth a stable ground and placed within it rivers and made for it firmly set mountains and placed between the two seas a barrier? Is there a deity with Allah? [No], but most of them do not know.
Quran 27:61
He released the two seas, meeting [side by side]; Between them is a barrier [so] neither of them transgresses. So which of the favors of your Lord would you deny? From both of them emerge pearl and coral.
Quran 55:19-22
Another reference to "the two seas" (bahrayn) is found in the story of Moses and his servant.
And [mention] when Moses said to his servant, "I will not cease [traveling] until I reach the junction of the two seas or continue for a long period." But when they reached the junction between them, they forgot their fish, and it took its course into the sea, slipping away.
Quran 18:60-61
The story of Moses and his servant is one of four stories in Surah al-Kahf. Modern academic scholarship has identified antecedants of each story in the lore of late antiquity. This particular story is almost unanimously considered to derive from a legend about Alexander the Great and his search for the water of life. For details see the section on the four stories in Surah al-Kahf in the article Parallels Between the Qur'an and Late Antique Judeo-Christian Literature.
It may further be compared to the ancient Akkadian myth of the Abzu, the name for a fresh water underground sea that was given a religious quality in Sumerian and Akkadian mythology. Lakes, springs, rivers, wells, and other sources of fresh water were thought to draw their water from the Abzu underground sea, while the Ocean that surrounded the world was a saltwater sea. This underground sea is called Tehom in the Hebrew Bible. For example, Genesis 49:25 says, "blessings of the heavens above, and Tehom lying beneath". Wensinck explains, "Thus it appears that the idea of there being a sea of sweet water under our earth, the ancient Tehom, which is the source of springs and rivers, is common to the Western Semites". Similarly in Greek mythology, the world was surrounded by Oceanus, the world-ocean of classical antiquity. Oceanus was personified as the god Titan, whose consort was the aquatic sea goddess Tethys. It was also thought that rainfall was due a third ocean above the "Firmament of the Sky" (a vast reservoir above the firmament of the sky is also described in the Genesis creation narrative).
Whether the two seas mentioned in the Qur'an referred to these mythological seas or a more general inviolable barrier between bodies of salt and fresh water, critics argue that the verse in question is scientifically wrong.