The sand bar includes the two most threatened habitats in the protectorate: the sand dunes and the salt marshes. These habitats support some of the highly threatened species found along the Mediterranean coast of Egypt. No less than 51 plant and 13 mammal species have been recorded in these habitats. The salt marshes are of major importance for two subspecies of birds (the Lesser Short-toed Lark Calandrella rufescens nicolli and Motacilla flava pygmaea) endemic to Egypt.

The brackish and fresh waters of the Lake are the most important habitat types in the protectorate as they support all fishing activities as well as being important for large populations of waterfowl.

Intertidal mudflats are utilized extensively by many wading birds both during migration and in winter, and provide important resting places for the many thousands of other water birds that pass through the region.

Reed swamps form the greatest biomass, and are of particular importance as a breeding habitat for several water birds, supporting sizeable populations of some 15 breeding species as well as holding one of the largest populations in the Western Palearctic of the Purple Gallinule Porphyrio porphyrio and the Little Bittern Ixobrychus minutus.

From the perspective of species richness, some of the islets in Lake Burullus (e.g. El-Kom El-Akhdar and Dechimi) harbor the largest numbers of species of flora and fauna, and are characterized by high species and microhabitat diversities. About 89 species of plants, and many birds, mammals and reptiles have been recorded on these islets. They also include many of the rare and unique species which are of limited distribution elsewhere in the region.