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The current practice of water resources use in irrigated agriculture in the Republic of Azerbaijan has some specific features and causes problems in the management of irrigation systems of different levels, associated with the existing land use and cropping patterns in the country. This article substantiates the need to implement a system of measures for improving water resources management in irrigation aimed to prevent the further depletion of their reserves through modernization of irrigation-reclamation systems and improvement of agricultural practices. The article proposes principles for protection of water resources and measures to mitigate the aftereffects of intense irrigation under anticipated increase in the internal consumption of freshwater and a decrease in transboundary river inflow into the Republic of Azerbaijan in the context of increasing water intake in the countries in Kura- Aras basin and global climate changes.