The present study was conducted in Lake Manzala at Ashtoum El-Gamil Protected Area that locates in the northeastern part of the lake. Subsurface water samples for phytoplankton investigation were collected monthly from four sites during October 2013-September 2014. A list of 109 species was identified and classified into a specific level. The recorded species belonged to 59 genera and was classified into seven Phyla. Bacillariophyta was the most diversified group with the highest number of the recorded species (51 species, 26 genera), constituting 47% of the phytoplankton community. The three Phyla; Chlorophyta, Dinoflagellata, and Cyanobacteria contained a relatively close number of species (17, 16 and 13 species, respectively) and occupied the second order, collectively belong to 27 genera, constituting 43% of the phytoplankton community. The other three Phyla; Euglenozoa, Charophyta, and Ochrophyta (Dictyochophyceae) were represented by a low number of species (5, 5, and 2 species, respectively forming 10%), and each belongs to two genera. The composition of the phytoplankton community in Lake Manzala was greatly influenced by the relatively high inflows of both freshwater and nutrients into the lake, producing a phytoplankton community dominated by Chlorophyta, and Cyanophyta which had fresh and brackish water affinity. In addition, receiving seasonal backflows of seawater from the Mediterranean Sea and Suez Canal enhanced the Bacillariophyta and Dinoflagelata species.