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The work concerns the application of spectral indexes (NDVI, SAVI and other types of spectral indexes) for monitoring and evaluation of the plant communities of desertified Amudarya river delta plant communities. The described approach includes the multi-level spatial model of the landscape transformation with desertification, soil erosion, soil salinity increasing, climatic changes to improve the adequacy of the remote sensing methods for complicated and non-stable post-deltaic ecosystems of the Aral Sea region. The key role of the geomorphological and pedological analysis for the spatial model implementation had been shown. Some geostatistical techniques had been used to link general data on vegetation cover calculated from remote sensing information with the type of the plant community, with consequent clarification of the vegetation map using both succession-based model approaches and field data.