In 1918, the Russian government decided that the two rivers that fed the Aral Sea, the Amu Darya in the south and the Syr Darya in the northeast, would be diverted to irrigate the desert, in order to attempt to grow rice, melons, cereals, and cotton. This was part of the Soviet plan for cotton, or "white gold", to become a major export. This did eventually end up becoming the case, and today Uzbekistan is one of the world's largest exporters of cotton.

The irrigation canals began to be built on a large scale in the 1940s. Many of the irrigation canals were poorly built, letting water leak out or evaporate; from the Qaraqum Canal, the largest in Central Asia, perhaps 30 to 75% of the water went to waste. Today only 12% of Uzbekistan's irrigation canal length is waterproofed.

By 1960, somewhere between 20 and 60 cubic kilometers of water were going each year to the land instead of the sea. Thus, most of the sea's water supply had been diverted, and in the 1960s the Aral Sea began to shrink. From 1961 to 1970, the Aral's sea level fell at an average of 20 cm a year; in the 1970s, the average rate nearly tripled to 50–60 cm per year, and by the 1980s it continued to drop, now with a mean of 80–90 cm each year. After seeing this, the rate of water usage for irrigation continued to increase: the amount of water taken from the rivers doubled between 1960 and 2000; cotton production nearly doubled in the same period.

The Aral Sea fishing industry, which in its heyday had employed some 40,000 workers and reportedly produced one-sixth of the USSR's entire fish catch, pretty much disappeared; so did the muskrat trapping in the deltas of Amu Darya and Syr Darya, which used to yield as much as 500,000 muskrat pelts a year.

The disappearance of the lake was no surprise to the Soviets; they expected it to happen long before. As early as in 1964, Aleksandr Asarin at the Hydroproject Institute pointed out that the lake was doomed explaining, "It was part of the five-year plans, approved by the council of ministers and the Politburo. Nobody on a lower level would dare to say a word contradicting those plans, even if it was the fate of the Aral Sea."

The reaction to the predictions varied. Some Soviet experts apparently considered the Aral to be "nature's error", and a Soviet engineer said in 1968 that "it is obvious to everyone that the evaporation of the Aral Sea is inevitable." On the other hand, starting in the 1960s, a large scale project was contemplated to redirect part of the flow of the rivers of the Ob basin to Central Asia over a gigantic canal system. Refilling of the Aral Sea was considered as one of the project's main goals. However, due to its staggering costs and the negative public opinion in Russia proper, the federal authorities abandoned the project by 1986.