Abstract. The aim of this paper is to identify the general trend of changes and the basic requirements of the most important lagoon system of the Black Sea, on the basis of critical analysis of existing data. A more coherent set of data sampled after 1988 on the basis of some intensive and extensive study and research programmes, including the main trophic parameters and the most representative structural and functional features of this complex of ecotonal lakes, is comparatively analysed together with more fragmentary data previously existing. The structural and functional changes within this complex of lakes were analysed based on 31 most representative variables belonging to the main abiotic and biological compartments of the two main lakes, Razim and Sinoe: dissolved organic carbon, dissolved oxygen, trophic state index TSI, nutrient content and ratio, salinity, chlorophyll, phytoplankton, zooplankton, submerged macrophytes, zoobenthos, fish and birds. Two stages were distinguished in the main structural changes, including morphometric connections with the Danube River and the Black Sea and hydrochemistry and its effects on communities. These transitions were associated with two main driving forces, water desalinisation and rapid eutrophication, and with other two kinds of man-induced changes, local hydrotechnical buildings and long-distance variables operating over the entire Danube River watershed. The information support system for sustainable management of the Razim-Sinoe Lagoon Complex as a part of the Danube Delta Biosphere Reserve, integrating existing data from research programmes and an integrated monitoring system for new data is a final conclusion on further needs.