In Arabic, bahrayn is the dual form of bahr ("sea"), so al-Bahrayn means "the Two Seas". However, which two seas were originally intended remains in dispute.[7] The term appears five times in the Qur'an, but does not refer to the modern island — originally known to the Arabs as "Awal" — but rather to the oases of al-Katif and Hadjar (modern al-Hasa).[7] It is unclear when the term began to refer exclusively to the Awal islands, but it was probably after the 15th century.

Today, al-Hasa belongs to Saudi Arabia and Bahrain's "two seas" are instead generally taken to be the bay east and west of the island,[8] the seas north and south of the island,[citation needed] or the salt and fresh water present above and below the ground.[9] In addition to wells, there are places in the sea north of Bahrain where fresh water bubbles up in the middle of the salt water, noted by visitors since antiquity.[10]

An alternate theory offered by al-Ahsa was that the two seas were the Great Green Ocean and a peaceful lake on the mainland;[which?] still another provided by al-Jawahari is that the more formal name Bahri (lit. "belonging to the sea") would have been misunderstood and so was opted against.[9]