Along the Mediterranean Coast of Egypt, 5 natural lakes are present: Mariut (Western Coast), Edku, Burullus and Manzala (Deltaic Coast) and Bardawil (Sinai Coast). The floristic features, habitats and plant communities of these lakes were analyzed. A total of 402 species belonging to 248 genera and 68 families were recorded in these lakes. The grasses have the highest contribution to the total flora, followed by composites and chenopods. Floristically, the richest lake was Burullus. The life forms of the recorded species indicated the predominance of therophytes followed by geophytes–helophytes, chamaephytes and hemicryptophytes. The global distribution of the recorded species indicated that seven species are endemic and most of the recorded species are monoregionals. Multivariate analysis is used to analyze the vegetation and environmental variables of 298 sampled stands in Lakes Mariut and Edku. 17 vegetation groups in Lake Mariut and 15 in Lake Edku were identified. These groups were separated along the prevailing moisture gradient from the shoreline to the open water The plant communities were compared with those of Burullus, Manzala and Bardawil Lakes.