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The large wetland represented by the Danube Delta is characterized by various environmental conditions (terrestrial, swampy or aquatic), showing, among other characteristics, a rich and diversified vegetation. Its growth and distribution are controlled by the season and by the frequency of floods, and are influenced by erosion and accumulation processes. Topo-geodetic mapping of emerging aquatic vegetation is necessary for a better knowledge of its evolution and of the changes that occur in the aquatic ecosystems. Particular attention focused on the formation and movement of fixed and floating reed beds on lakes. By monitoring their dynamics, it would be possible to track the processes of obstruction or blocking channels and entrances in lakes, phenomena with negative consequences on navigation, fishing and tourism activities. Topo-geodetic assessment of the stability of the reed associations in the Danube Delta’s lacustrine complexes and ecosystems is important, because these environments are the main habitats for wildlife existing there. Topo-geodetic mapping has been aimed at delineating the aquatic vegetation fields which have been continuously expanding in the last period, leading to the suffocation of the aquatic life of the lake ecosystems, due to oxygen deficiency in the water. The water bodies under our survey are: Babina Lake, Ciortic (Dracului) Lake, and Corciuvate (Rădăcinoasele) Lake, located in the central-western part of Matiţa-Merhei aquatic complex. The study carried out on the evolution of the vegetation areas within the three lakes was performed for two distinct periods, namely 2006 and 2018. After the processing and interpretation of the available data, a significant decreasing trend of the free water surface was evidenced, associated with an increase of the vegetation covered areas. The most important free water surface reduction was observed in Ciortic (Dracului) Lake (37.07%), then Babina Lake (13.38%) and Corciuvate (Rădăcinoasele) Lake (5.23%).