We analyzed the vegetation of Lake Burullus at the deltaic Mediterranean coast of Egypt, the sand bar between its northern shore and Mediterranean Sea, the water courses that drain into the lake and the wetland around it. Our ultimate aim was to identify threatened species and communities and the environmental factors that affect their distribution in order to formulate a plan for their conservation. The total number of the recorded species was 197 (100 annuals and 97 perennials), including 12 floating and submerged hydrophytes. Three species are endemic to Egypt: two annuals (Sinapis arvensis subsp. allionii and Sonchus macrocarpus) and one perennial (Zygophyllum album var. album). Thirty-four species are rare allover Egypt (15 annuals and 19 perennials). The lake area included 10 types of habitat (sand formations, salt marshes, lake cuts, terraces, slopes, water edges and open water of the drains, islets, shores and lake). The vegetation was classified into 13 groups (i.e., plant communities). Six groups were dominated or co-dominated by the common reed (Phragmites australis); these groups occupied a wide environmental gradient from xeric to hydric habitats. Five other groups were dominated by halophytic species (Arthrocnemum macrostachyum, Suaeda vera, Sarcocornia fruticosa, Halocnemum strobilaceum and Salsola Kali). The remaining two groups were dominated by the emergent Typha domingensis and the submerged Potamogeton pectinatus. Moisture, salinity and sedimentation were the main factors that governed the plant succession in this wetland.