Wadi El Rayan is located in the African Sahara ecoregion of the Palearctic eco-zone, the world's largest hot desert. The total area of Wadi El Rayan is 1759km(2). The objective of the present study is to enrich the knowledge on the vegetation cover along the shores of Wadi El Rayan lakes and to identify the different threats, underlying causes and recommended solutions for the conservation of natural vegetation cover in Wadi El Rayan Protected Area (WRPA). Based on field surveys, we found that current pressures of human activities on natural vegetation include overgrazing, irresponsible tourism, land encroachment, water pollution, water over-use, fire, and habitat change and destruction. The reduction of water levels due to decreased water incoming is considered the main threat facing ecosystems and biodiversity in the lakes area. We found that the perimeter of the lower lake has decreased from 48.6km(2) in 2007 to 34.09km(2) in 2013 (a loss of 29.8 % of the total lake area), due to lake decreased water level. The most underlying causes of vegetation loss in the study area were found to be the lack of awareness, weak law enforcement, lack of suitable strategies, weak financial support and lack of stakeholders' cooperation. Survey results show that vegetation cover in the area of the connecting channel and northeastern of the lower lake represents the highest impacted area by human pressures compared to other locations. Moreover, the role of WRPA is important in achieving good cooperation between governmental authorities, local community, and owners of different economic activities and in finding new ways to improve potential future cooperation with other stakeholders. We also provide some suggested activities for conserving vegetation cover in WRPA.