Seasonal structure of phytoplankton in Lake Qarun was estimated. A total of 50 algal taxa related to 4 classes were identified: Bacillariophyceae (36 taxa), Dinophyceae (9 taxa), Cyanophyceae (3 taxa) and Chlorophyceae (2 taxa). It was dominated by only 5 spp of diatoms (Cyclotella glomerata, C. kutizingiana, Nitzschia closterium, N. fonticola. and N. frustulum var. perpusilla) constituting about 89.44% from the diatoms density and 5 spp of dinoflagellates (Exuvaiella apora, Gymnodinium orientalis, G. smile, Peridinium incospicum and Prorocentrum micans) forming about 96.7% from the dinoflagellates density. Different diversity indexes were applied to estimate species diversity, richness, evenness, redundancy and the dominance for the predominant species. The results were compared with the previous data and discussed with the effect of accumulated pollutants drained into the lake. Biodiversity studies indicated that the lake biota is affected by the destructive action of these pollutants, and some of the dominant species are known as one of toxin-producing phytoplankton.