Phytoplankton samples were collected during February, April and June 2004 at fourteen stations. Phytoplankton community represented by 117 species within 66 genus from five groups (Bacillariophyceae; Dinophyceae; Chlorophyceae; Cyanophyceae and Euglenophyceae). There were some fresh, brackish, and marine species. Bacillariophyceae was the most dominant group (71 species) contributing 94.2% of the total phytoplankton counts. The phytoplankton community is generally more productive at stations 1, 2, 3, 4 and 5 that receiving discharge water from El-Tabia pumping station (Stations 1, 2, 3 and 4)  and Lake Edku (St. 5). A gradual decrease was seen in phytoplankton density seawards. The major phytoplankton peak was observed at most stations during June (average 5535 x 10³ unit.L^-1). Skeletonema costatum was the most dominant species; it was formed 51.3%, 41.3% and 60.4% of the total phytoplankton, respectively during February, April and June. The effect of discharge water was more pronounced at St. 4 in front of El-Tabia pumping station. Species diversity index displayed narrow temporal and spatial variations from 1.02 to 2.85 nats. Throughout the bay, station 3 sustained the lowest diversity index (1.38 nats), while station 14 recorded the highest value (1.95 nats).