Amu Darya and the Syr Darya, flow into the Aral Sea and form the Aral Sea Basin. The basin comprises southern Kazakhstan, most of Kyrgyzstan and Turkmenistan, practically the whole of Tajikistan and Uzbekistan, as well as the northern part of Afghanistan and a small portion of Iran. The Amu Darya has an average annual water flow of 74 km³, making it Central Asia's mightiest river. Its origins are the rivers Panj and Vakhsh in Tajikistan and Afghanistan. After their confluence, the Amu Darya first forms the border river of Afghanistan with Tajikistan and then with Uzbekistan and Turkmenistan. It crosses Turkmenistan and flows into Uzbekistan, where it reaches the southern shore of the Aral Sea. Its total length from the source of the Panj is 2 540 km. Its catchment area ranges between 465 000 km² and 612 000 km², depending on how it's calculated. The basin also includes the Sherabad, Surkhan Darya, Kashka Darya and Zarafshan rivers, although the latter two do not discharge into the Amu Darya.

The Syr Darya, whose source is that of the Naryn, is considerably longer at 3 019 km, but its annual flow is much smaller: on average 37 km³ per year. The Naryn originates in Kyrgyzstan, flows into the Ferghana Valley and becomes known as the Syr Darya after it joins the Kara Darya. It crosses Uzbek and Tajik territory before it flows again into Uzbekistan and then into Kazakhstan, where it ends in the northern part of the Aral Sea. The Syr Darya basin is estimated at 782 617 km².

Both rivers are fed mainly by snow and glacier melt in the high mountain regions of Kyrgyzstan, Tajikistan and Afghanistan. This leads to high seasonal variability in water flow with peaks in spring and summer. The flow can vary considerably year-to-year due to weather conditions. In wet years, the Amu Darya has reached 96.3 km³ (1969), while its flow shrank to 52.8 km³ in 1947. Similarly, the Syr Darya flow was only 18.3 km³ in 1917, while it reached 72.5 km³ in 1921.[, UNECE 2007, UNECE 2011] In order to regulate water flows and have water available when needed, a sophisticated system of dams, reservoirs and hydro-facilities has been built over the past century. The operation and maintenance of this infrastructure, most of which is of transboundary significance, requires sound coordination of the involved national agencies or a transboundary regulatory framework.

Aral Sea Basin
Left: Aral Sea Basin before 1960, Right: Aral Sea Basin today
Average seasonal flow of the Amu Darya
Amu Darya Basin
Amu Darya’s linear scheme
Average seasonal flow of the Syr Darya
Syr Darya Basin
Syr Darya’s linear scheme