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The phytoplankton community composition and bivolume were monthly studied in relation to polluted freshwater and saline sea water intrusion into Lake Manzala. The dominant classes in Lake Manzala were chlorophytes, diatoms and cyanoprokaryotes. The three groups altogether constitute more than 90% and 89% of the total phytoplankton abundance and total number of taxa, respectively. Other groups were marginally present like prasinophytes, cryptophytes, chrysophytes, euglenophytes and dinophytes. On biovolume basis, diatoms dominated the phytoplankton communities, whereas, based on cell number, the chlorophtes exclusively dominated the phytoplankton communities year round. The three dominant classes were dominated by single celled, Dyctiusphaerium pulchellum (chlorophytes), Cyclotella menenghiniana (diatoms), Microcystis aeruginosa and Tetrachloris merismopoides (cyanoprokaryotes). Six functional groups were mainly represented which are diatoms (D and B), chlorophytes (X1, F and J) and cyanoprokaryotes (X1 and M). These groups are typical representatives of highly mixed, turbid with high nutrient ecosystems. Both the ordination analysis and the correlation matrix revealed an independence of phytoplankton communities with the trophic status of the lake.