During the second cold period (antiquity), the Zerayshan deviated to the left (equatorward). The flow along the Makhan Dar'ya then ceased and the settlements which depended upon this water became deserted. The whole Makhan Dar'ya delta became uninhabitable at this time.
During the second warm period (early Middle Ages), the river once again deviated to the right (northward). Accordingly, the territory to the west of Bukhara became watered again. One of the many remains dating from this time is the Varakhsha fortress (Shishkin, 1940, 1950).
Dzens-Litovskii (1936, p. 22) assumes that in the sixth century A. D. the northern part of what is now the cultivated strip of the Bukhara oasis was a swampy plain, the so-called Sufioni marshes, During the third cold period (late Middle Ages), the Zerayshan deviated to the left (southward). Accordingly, the land in the vicinity of the Varakhsha fortress became deserted, while the left bank of the Zerayshan became well watered. Here, beginning at Pendzhikent and continuing further downstream, an effective irrigation system was constructed and continued to function for a long time (particularly noteworthy were the Dargan canal and, to the south of it, the Manas canal).
The whole left bank of the river was densely populated at this time, and these medieval settlers left behind a great many monuments of various kinds. The southern part of the delta itself (the Karakul' oasis) was also well watered. In the time of Genghis Khan, this district was a vast stretch of lakes and swamps.
During the third (present) warm period, the Zerayshan tends to deviate to the right (poleward). The irrigation system based on the left-bank canals is thus now being disrupted. According to the data of Arandarenko (1889), the Manas irrigation ditch ceased operating sometime after the Timurid period. The Tyue-Tartar, Mirza-Aryk, and Polvan canals, which branch out from the right bank of the river, were maintained at a constant water level with almost no effort at all. The operation of dams and maintenance of the water level in the left-bank canals (the Sarazm-Any Kazan and Ayaz-Abat canals), on the other hand, turned out to be quite difficult for the agricultural population. The southern part of the delta became dry, the irrigated farmlands went into disuse, and the region became deserted. For example, along the Taikyr River, the last terminal
channel of the Zerayshan, there are enormous areas of cultivated land which stand neglected, and abandoned mazars [a kind of holy grave] and the ruins of adobe kibitkas [rude huts] are to be seen (Dzens-Litovskii, 1936, p.23).
This sequence of the migrations of the river is borne out by many data, in particular by the findings of archaeological-geomorphological studies. For example, it has been established that during the cold periods the Kutan Dar'ya and Zhana Dar'ya deltas, right down to the Akcha Dar'ya delta of the Amu Darya were densely populated, as in ancient times, when the so-called Kokcha-Tengiz culture was widespread in this region, and in the late Middle Ages, from the twelfth and thirteenth centuries on.
The main occupation of the people inhabiting these areas was irrigation farming, which could only have been possible using the distributary waters of the Syr Darya. This indicates that in ancient times and in the late Middle Ages the Amu Dar'ya deviated to the south. However, the more the cold phase of the climatic cycle gave way to the succeeding warm phase, the less water there was in the left-bank distributaries of the Syr Dar'ya and the more the channels became filled up with deposits.