In ancient times the river was dammed by at least two large works: one lies near Amuy, at the beginning of the lower course, today called Carjuy, and the other was at Gurganj where the river bifurcated into two beds. Al-Muqaddasi one of the most notable geographers and scholars of his time,originally from Al-Quds (Jerusalem) around 985 AD describes the Gurganj dam as an amazing work of engineering, built all of wood and resembling sea-works in wood and wickerwork.
Just above this point, the river's course splits: a small branch runs north to the Aral Sea, but another larger branch runs west, past the town of Gurganj, into a deep depression called the Sarykamysh, about 155 miles SW of the Aral Sea. This Sarykamysh depression lies about 100 metres deeper than the river's bed at Gurganj. From the Sarykamysh, a dried-up riverbed called the Uzboi runs through the Balkhan hills all the way to the Caspian Sea.
The Aral Sea's level is itself only about 20 metres deeper than river level at Gurganj. Everything depends on the river's level. In times when the larger branch of the Oxus emptied into the Sarykamysh then in effect it became the true basin of the Amu daya not the Aral Sea.
At the Sarkayamysh the larger part of the river's waters end, like those of other desert lakes: evaporating, without exit. However in times past when little irrigation-water was used upriver, the filled basin of the Sarykamysh overflowed and discharged through the Uzboy into the Caspian.
History of the river's several courses:
Present-day back to about 1575 AD: both Jaxartes and Oxus rivers (the Syr Darya and Amu Darya) run to the Aral Sea, as they do today. Around 1575, the Amu darya's course changed.
Evidence: Abulghazi Khan, born 1603 and ruled 1642-63, wrote that the course of the rivers changed thirty years before his birth. Anthony Jenkinson, British trader and diplomat, the envoy of Queen Elizabeth, and the agent of a company founded in England for trading with Moskovia wrote in 1558-59 describing how the Oxus ran in the Uzboi channel but no longer reached the Caspian Sea, and made the prediction that the demands for irrigation would soon lead to a complete desolation of the region.
From 1575 to 1221 AD (the date of the Mongol invasion) the Amu Darya discharged into both the Caspian and the Aral Seas--usually the main branch ran to the Caspian, but during at least one period, a side branch also ran to the Aral. Thus the seas were linked. There are perhaps four courses which this river seems to have followed at various periods. At this time, the river split just above the town of Gurganj; the main branch ran south of the town (coursing westward) filled the Sarykamysh (about 150 miles SW of the Aral Sea) ran through the Uzboi bed SE to a gap in the Balkhan hills (over 100 miles SE of Krasnowodsk) and discharged into the Caspian Sea opposite the group of islands called Oghurtcha or Aghyrtcha.
Evidence: 1) In 1392, Zahir al-din al-Mar'ashi a native of Mazandaran, describes in detail every waterway from Mazandaran to Khwarizm. 2) Shihab al-din 'Umar al-'Umari (d. about 1348) remarks on the authority of witnesses from Khwarizm "On Khwarizm borders ... a country ... Mangyshlaq, a steppe ... separated from the Djaihun (Oxus) by the Ak-Balkan hills north of Khurasan." 3) In the reign of Oldjaitu (1304-16) Hamdallah al-Mustaufi speaks of the caravan route from Gurgan by way of Dahistan (the modern-day Mashhah i Misriyan) to Gurganj, which had just been surveyed and was 110 fars (380 miles) in length between Dahistan and Gurganj--and says on the Uzboi there was a great waterfall, called in Turkish gurledi, roaring; and a side branch of the Amu Daya fell into the Aral Sea--and tells how the discharge of water of the Amu Daya into the Caspian had raised the sea's level so that the peninsula of Abaskun (Pliny's Socanda) was submerged. 4) The historians Marino Sanudo (1325) and al-Bakuwi (beginning of the fifteenth century) confirm this description.
The river changed its course in 1221 because the armies of Genghis Khan destroyed the great dam at Gurganj : record of ibn al-Athir, xii, 257. From the tenth century to 1221, the Amu Darya seems not to have flowed to the Caspian. However the records are vague and contradictory.
Evidence: the earliest is from ibn Khurdadhbih, but is vague because of variants in texts; Ibn al-Raqih at the beginning of the tenth century, tells a legendary and thus unverified story; ibn Rustah (writing between 903 and 913 AD) carefully describes the mouth of the river's main branch, showing that it discharged into the Sarykamysh. Istakhri (about 960 AD) says the river flows into the Aral Sea. Al-Ya'qubi (about 890) however says it falls into the Caspian.
Muqaddasi--the author of the description of the Gurganj dam--circa 985 AD, relates a legend according to which the Uzboi as the Oxus' main branch had once, long ago, carried water (ergo, it did not do so in Muqaddasi's day) and reached the town of Balkhan in Khurasan; however once the inhabitants of Kath (the pre- and early-Muhammedan capital, 30 miles east of Khiva) had diverted the whole course of the river to their easternmost branch for 24 hours, the river did not turn back to the Uzboi channel and the whole Balkhan region was laid waste by lack of irrigation.
According to Byzantine historians, this region then called Balaam was settled before the Muslim conquest as ot already had irrigation then, and the Amu Darya flowed into the Caspian. (It is not possible to settle an entire region without a major river to provide water.)
In high antiquity, Strabo (C.510) and Polybius (x,48) both mention a waterfall of the Amu Darya; this is probably the waterfall of the Uzboy mentioned by Hamdallah.
Evidence: Seleucus of Persia planned to connect the Caspian by a canal with the Black Sea, if a report of the exploration of the Caspian should be favorable. This took place not later than 282 B.C. Xenocles, the gazophylax of the archives of Babylon, had made accessible for study to Patrocles (the agent sent to study the issue) the original documents with observations by Alexander the Great's general staff concerning the problem. The purpose of the project was to develop trade. Strabo xi (c.509 and 518) quotes Aristobulus speaking of the transport of Indian merchandise on the "well navigable Oxus" (in the present day, the river is not navigable; the water-level fluctuates too much) to the Caspian and across the sea and thence through the Caucasus to the Euxinus or Black Sea . . . This plan of Seleucus' implies that the Oxus was known to discharge into the Caspian, else the whole project would fall to the ground. Hence, in the early third century BC the Amu Daya flowed into the Caspian.
Source: Ernst Herzfeld, Zoroaster and His World, vol II, 1947. Ernst Herzfeld, Professor of Oriental Archaeology at the University of Berlin.