The aeolian transport of dust, sand and salt is a common process in southern Kazakhstan, as well as in the Aral Sea region. Anthropogenic desertification and the desiccation of the Aral Sea have occurred in the basin since 1960. The whole area of the desiccated seafloor is now a new salt desert, and it became an active source of dust, sand or salt storms. The newly formed Aralkum desert was found to be the dominant source of aeolian sand, dust and salt aerosols. Additionally, the most frequent storms were observed in Pre-Aral Karakum and Kyzylkum deserts, where these storms occurred from 40 to 110 days average per year. Aeolian sands and dusts flowed mainly from eastern and north-eastern to the western and south-western directions. The highest amount of sand transportation was observed at the Aral Sea meteorological station. The lowest amount was at the Kazaly meteorological station. Furthermore, transported sand mass has increased at this station during last decade. Most meteorological stations found three maximums of sand and dust transportation, namely in 1966–1970, 1984–1986, and 2000–2002, that is, three periods, like a cycle about every 15 years. Overall, most of the meteorological stations showed the slight decrease in sand and dust transportation that may be explained by fixing sand control measures and other activities which have been done against deflation processes in the region.