(The Shatt-al-Arab, formed by the confluence of the Tigris and Euphrates, did not exist in antiquity, when the Gulf extended farther to the north than at present; alluvial deposits gradually filled in the shallow sea.)
The expansion of Islam in the seventh century through both Mesopotamia and Persia did not eliminate the distinction of the two regions. Though politically unified under the Caliphate, this unity evaporated when the Caliphate fragmented. Moreover, the Shia branch of Islam, though a minority in most of the Islamic world, gradually became the majority in Iran. In the 16th century, Iranian Shiism was institutionalized under the Safavi shahs, while at about the same time Mesopotamia was brought under the rule of the Sunni Ottoman sultans.
The modern era in this region may be regarded as beginning with the dissolution of the Ottoman Empire after World War I. What at that time was still called Mesopotamia was apportioned to Britain. Iraq became quasi-independent in 1921, but British influence remained dominant, as it was in Iran. However, the negotiation framework of the specific boundary dispute along the Shatt-al-Arab goes back a few years previously, to the Constantinople Protocol of 1913, negotiated between the Ottoman Empire, Iran, Russia, and Britain, had defined navigation right in the Shatt-al-Arab in a way that ceded several islands to (British-influenced) Iran.
The Protocol also specified that the thalweg -- the center