Bardawil Lagoon is a source of wildlife and high-quality fish, so, it is imperative that it should be subject to continuous monitoring of both water quality and the phytoplankton composition. Samples were collected from ten sites representing different habitats of the lagoon, from summer 2017 to spring 2018. The water properties were determined; noticeable low concentrations of dissolved inorganic nutrients were recorded. A total of 106 species belonging to six groups were recorded, among them Bacillariophyta (69 species) and Dinophyta (26 species). The obtained results clarify that Bacillariophytes prevailed in the eastern sites of Bardawil; on the contrary, Dinophytes occupied the sovereignty in the western sites of the lagoon. The most abundant Bacillariophytes were Licmophora gracilis, Gyrosigma acuminatum, Fragilaria construens, and Nitzschia sigmoidea; which formed more than 50% of total abounded diatoms. While, Protoperidinium leonis, Prorocentrum gracile and Protoperidinium granii were the dominant Dinophytes, giving it maximum at El-Rewak. From reviewing previous studies on the lagoon, it becomes clear that the phytoplankton composition varied widely from previously recorded, including the dominant species and their rates of sovereignty, which reflected economically on its fish productivity. Besides, the water quality in Bardawil fluctuated from slightly-polluted to moderately-polluted according to the diversity index, as a result of the recent, noticeable increase in human activities, especially fishing, which will be in turn reflected in the environment. Therefore, continuous follow-up through ecological assessment and monitoring studies of Bardawil became an urgent necessity.