Abstract Wadi El Rayan is located in Egypt in the Sahara ecoregion the Palearctic ecozone (the world’s largest hot desert). The total area of Wadi El Rayan is 1759km2. The aim of this work was to study the ecosystems, compare species composition, species richness and species diversity of the study sites in the Wadi El Rayan protected area and the distributions of plants in the different landform. The field observations found that there is a low diversity and number of plant species around the lakes, in particular a decline in vegetation cover in accordance with a dramatic decrease in the water level in the lakes compared to earlier studies. The reduction of water levels due to decreased water supply is considered the main threat facing ecosystems and biodiversity in the lake area which requires a continuous survey of flora and measures to be implemented to conserve the natural vegetation in the area. Based on investigations of the spontaneous flora of Wadi El Rayan in 2018, 18 taxa of vascular plants were recorded. This inventory was compared with published records of investigations made in 1998, 2002 and 2014. A total of 18 vascular plant species belonging to 14 families were recorded in the wetland and desert ecosystems around the lakes of Wadi El Rayan. The vegetation mainly consists of sparsely distributed xerophytic and halophytic plants except in the wetland ecosystem around the lakes where it is characterized by some hydrophytic and halophytic plants. The family with the highest number of species was Poaceae followed by Zygophyllaceae. The results showed that a higher number of species was recorded from the Lower Lake (13 species) than the Upper Lake (10 species) and (5 species) for the connecting channel. The most frequently recorded species were Phragmites australis, Tamarix nilotica, Juncus rigidus and Alhagi graecorum: the first two species were the most successful species as they grow in a variety of ecosystems and habitats.