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The Central Asia has one of the most modified land cover under irrigation influence and related ecological problems. The study is devoted to analysis of water security in connection with land cover and land use changes in Fergana Valley with transboundary position in Central Asia at territories of Uzbekistan, Kyrgyzstan, Tajikistan within the Syr Darya river basin. The modern land cover of the Fergana valley differs significantly in terms of irrigation that causes geography of water scarcity, features and intensity of salinization and waterlogging. Geographical information system “Allocation of water resources for irrigation in Fergana valley” was used to elaborate scenarios of water shortage for irrigation and to define how significant the landscape structure, groundwater level and soil texture characteristics impact the differences in irrigation conditions, geography of water scarcity, manifestations of ecological problems. Assessment of current conditions for the development of irrigated agriculture allowed to reveal that the landscape complexes with a high risk of salinization and waterlogging occupy in the Fergana valley respectively 20 and 50%. The most acceptable scenario to avoid water deficit in unstable transboundary irrigation system of Fergana valley is differentiation and updating of irrigation norms according landscapes’ characteristics, optimization of crops’ composition with the transition to the cultivation of horticulture plantations and winter crops. That will allow to reduce twice the proportion of land to water demand and to enhance up to 80 % efficiency of irrigation techniques. The results of study will be presented in the further volume of the IGU/LUCC Atlas.