The water resources in the Aral Sea region consist of renewable surface and groundwater, as well as return water from anthropogenic use (wastewater and drainage water). There are two major river basins located in the Aral Sea Basin: the Syrdarya in the north, and the Amudarya in the south. The Zeravshan river, a former tributary of the Amudarya, has a position between these two major rivers.

A feature of the region is the division of it's territory into three main zones of surface runoff:

(a) the zone of flow formation (upper watersheds in the mountain areas),
(b) the zone of flow transit and it’s dissipation,
(c) the delta zones.

As a rule, there is not a significant level of anthropogenic changes in the zone of flow formation, but due to construction of big dams and water reservoirs on the border of this zone, the downstream run-off regime is changing significantly. Within the zone of flow transit and dissipation the run-off and the whole hydrological cycle are changing in consequence of interaction between rivers and territory. This interaction is characterizing by water withdrawal from river to the irrigated areas and the loading of return flow to the river with salt and agricultural chemicals.

In terms of water availability the Syrdarya is the second most important river in Central Asia but the largest in terms of length. From the Naryn headwaters its length is 3019 km, with a catchment area of 219 thousands km². Its headwaters lie in the Central (Interior) Tien-Shan mountains. The river is known as the Syrdarya after the point where the Naryn joins with the Karadarya. The river has glacial and snow feeding, with a prevalence of the latter. The water regime is characterized by a spring-summer flood, which begins in April. The largest discharge is in June. About 75.2% of the Syrdarya run-off originates in the Kyrgyz Republic. The Syrdarya then flows across Uzbekistan and Tajikistan and discharges into the Aral Sea in Kazakhstan. About 15.2% of the flow of the Syrdarya is formed in Uzbekistan, about 6.9% in Kazakhstan, and about 2.7% in Tajikistan.

The Amudarya is the biggest river in Central Asia. Its length from the headwaters of the Pyandzh to the Aral Sea is 2540 km, with a catchment area of 309 thousands km². It is called Amudarya from the point where the Pyandzh joins with the Vaksh. Three large right tributaries (Kafirnigan, Surhandarya and Sherabad) and one left (Kunduz) flow into the Amudarya river within the middle reach. Further downstream towards the Aral Sea it has no tributaries. It is fed largely by water from melted snow, thus maximum discharges are observed in summer and minimum ones in January-February. Such availability of the flow within a year is very favorable to the use of the river water for irrigation. While crossing the plain, from Kerky to Nukus, the Amudarya loses the majority of its flow through evaporation, infiltration and withdrawal for irrigation. In terms of sediment the Amudarya carries the highest load of all the rivers in Central Asia and one of the highest levels in the world. The main flow of the Amudarya river originates on the territory of Tajikistan (about 74 %). The river then flows along the border between Afghanistan and Uzbekistan, across Turkmenian territory and then again returns to Uzbekistan where it discharges into the Aral Sea. About 13.9% of Amudarya water is formed on Afghan territory and in Iran. About 8.5% of the Amudarya flow is formed in Uzbekistan.

The total mean annual flow of all rivers in the Aral Sea Basin is estimated as about 116 km³. This amount comprises the flow of the Amudarya at 79.4 km³/year and the Syrdarya at 36.6 km³/year. In accordance with flow probabilities of 5% (high wet years) and 95% (dry years), the annual flow ranges from 109.9 to 58.6 km³ for the Amudarya river, and from 51.1 to 23.6 km³ for the Syrdarya river, respectively.

Surface water resources in the Aral Sea basin (mean annual runoff, km³/year)

Along the two rivers, the many intakes, which serve the major irrigation schemes, continuously reduce the volume of the remaining run-off in the rivers and inflow into the Aral Sea. As flow has diminished, the quality of the remaining water has worsened because of the discharges of saline and polluted drain effluent from irrigated areas and the residues of agro-chemicals, which leach into the drainage systems and mix with the waters of the rivers. Besides this non-point source pollution from agriculture, consisting of salt and agro-chemical residues, there is also point-source pollution from industrial and municipal wastes, especially from metropolitan areas.

The trend of the river water quality with respect to salinity is negative. The salinity level increases in time and along the river, especially in the middle and lower reaches of the river. At the end of the 1960s the mineralization of water did not exceed 1.0 g/l , even in the lower reaches. Now it varies from 0.3-0.5 g/l in the upper reaches to 1.7-2.0 g/l in the lower reaches. The highest values occur in March and April in the upper reaches, and around May in the lower reaches. An explanation for these differences could be the leaching procedures on the irrigated areas. Apart from the salinity levels, given in g/l, the chemical composition of the river water determines its suitability for irrigation. The value often used to express the risk of developing alkalinity is the SAR (Sodium Adsorption Ratio), which is expressed in meq/l0.5. An analysis of available data showed that the SAR normally ranges from 0.5-7 meq/l0.5 at most gauging stations. These values indicate that, in general, the water is still suitable for irrigation. It is necessary to mention that during last few years the river water quality has stabilized due to reduction of effluent disposal.

During the years since independence from the Soviet Union there has been implemented a strict limitation of water allocation between the countries and increasing attention to ecological aspects. This has led to some improvement of water quality. It can be seen from the figire that water mineralization in the low reaches of the Amudarya has reduced and has not exceed the permitted limit (1.0 g/l).

Variations of water mineralization along the Amudarya river

There are many natural lakes in the mountainous areas and ravines of Central Asia. The mountain lakes are of various origins. The majority of large lakes occupy basins which are the result of tectonic activity (Issuk-Kul, Song-Kel, Chetir-Kel, Karakul, Sarichelek). Lakes originating from landslides due to earthquakes are the Sarez and Yashinkul in the Pamir mountains. Numerous lakes are of glacial origin; one of the largest is the Zorkul, located at 4125 m in the Eastern Pamir. Karst lakes are also present. In the mountains, lakes are usually freshwater or slightly saline, depending on the quality of in-flowing water. The lake regime of the region requires further study.

The majority of lakes located in the lowlands owe their origin to the erosion-accumulation activity of rivers in an arid climate. Generally, lowland lakes are shallow with low shores and have heavy vegetation of reeds and rushes. They are often surrounded by saline soil (solonchak) and sand. Given enough precipitation, many of these lakes would turn into temporarily running waters, which would leave behind dry river beds over time. Lowland lakes may be either saline or freshwater. Initial assessments of freshwater reserves in mountain and lowland lakes suggest a volume of 60 km³.

Due to the outflow of drainage waters to closed basins (no outlet), many human-induced lakes have come into existence. Most of these are shallow, however, Lake Sarikamish (at the lower reaches of the Amudarya) and Arnasay (at the middle reach of the Syrdarya) are the largest human-induced lakes in the region. Due to the limited capacity of the river channel of the Syrdarya below the Chardara reservoir (on the border between Kazakhstan and Uzbekistan), excess volumes of water are discharged into the Lake Arnasay during high water years. In the last few years, this practice has been common also in winter as a result of the energy releases from the Naryn-Syrdarya hydropower cascade. Estimates put the volume of water resources in human-induced lakes at 40 km³. However, making use of these waters would require considerable pumping. Also, the waters are highly mineralized. The best future use of these waters may be for fishery and biodiversity conservation.