The Aral Sea is a part of a self-regulating hydrological system. It receives water from the two largest rivers in Central Asia, the Amudarya and Syrdarya, and the sea water evaporates into the atmosphere. Changes in this balance have a primary effect on the water level of the sea. These rivers flowing to the Aral have exhibited extremely uneven flow from one year to the next. For example, during a 60-year period, the Syrdarya's annual flow ranged from 22 to 57 km3, with a mean value of 34 km3; the Amudarya's flow ranged from 48 to 101 km3,with a mean value of 63 km3. A ‘periodicity’ of low-flow and high-flow periods has been observed to last 10–12 years. Clearly, the decrease of river flow to the sea results in a drop in sea level, in a reduction of sea surface area and volume, and in changes in other characteristics of the sea.

Irrigation farming in the Aral Sea basin began at least as early as 4000 BC. The local population of this region, like those in the valleys of the Tigris, Euphrates and Nile rivers, shared the experiences and knowledge accumulated over generations about the use of regional water resources, and about how to carry out irrigation farming in river floodplains and deltas in arid areas without disturbing the balance of nature.

The major disturbance of the long-lasting natural balance between ecological change in the Aral basin and the sea began early in the twentieth century as a result of human activities. Before then, the sea was abundant in water and even had a tendency to rise, despite the onset of intensive colonization of the region by Tsarist Russia.