El Mex Bay is an estuarine area; it is one of the “hot spots" on the Egyptian Mediterranean Coast. It is located west of Alexandria City. It is influenced by different pollutants from the El Umum Drain water, impacting the water quality. Phytoplankton community structure was monitored as well as different water types over two-decade intervals. The first was recorded monthly from April 2003 to April 2004, while the second was recorded seasonally from winter 2020 till spring 2021 to monitor the changes that have occurred in this region. The phytoplankton abundance in El Mex Estuary showed significantly higher eutrophication during the first period (1.243x10⁶ units l^-1, 82 genera, and 201 species) than the second one (0.946x10⁶ units l^-1, 70 genera, and 123 species); moreover, the community structure differs in terms of phytoplankton class abundance. Baccillariophyceae dominated the phytoplankton community in the two periods, representing 87.18 (39 genera & 96 species) and 77.0% (36 genera & 69 species), respectively. However, Dinophyceae contributed 3.41 (10 genera & 30 species) and 9.2% (12 genera &16 species), respectively. Cyanophyceae are shared by 0.7 (10 genera & 18 species) and 4.47% (8 genera & 10 species), respectively. The phytoplankton abundance at El Umum Drain recorded remarkably higher eutrophication during 2020– 2021 (1511.3x10³ units l^-1, 64 genera & 147 species) than that in 2003– 2004 (0.352x10³ units l^-1, 70 genera & 123 species); furthermore, the community structure differs. The trophic status was ascertained and discussed using a variety of metrics, including phytoplankton abundance, diversity indices, and others. Based on these measurements, El Mex Estuary was found to be highly eutrophic and significantly contaminated to differing degrees