The excessive water use in Central Asian countries has caused an environmental disaster in the Aral Sea. In this regard, they need to improve the efficiency of the use of shared water resources to overcome their environmental and economic difficulties. Accordingly, the twin objectives of this study were firstly to analyse the challenges for the use of water resources in the Aral Sea Basin and secondly to estimate the agricultural water use efficiency according to the crop types and irrigation methods. The results showed that the economic efficiency of water use in Central Asian countries was lower than that of other Asian countries. Finally, this study illustrated that the selection of crop types and irrigation methods can improve the quantitative and economic efficiency of water use. However, a clear preliminary outline of interactions is necessary to avoid failure of coordination and collaboration for a regional win-win approach. In such an outline, this study will deliver valuable information on water efficiency in the Aral Sea basin.