El-Mex Bay is a semi-sheltered coastal embayment located west of Alexandria, the Egyptian Mediterranean Sea. It is considered as a hot spot area receiving industrial, agricultural, and domestic wastes from the adjacent Lake Mariut through El-Umum Drain. To evaluate the water quality of the bay, phytoplankton and macroalgae as biological tools were investigated seasonally concerning physicochemical parameters from 2018 to 2019. The results indicated that the Bay harbored a diversified phytoplankton community (162 species), comprising 99 freshwater forms, 38 marine, 22 euryhaline, and only 3 brackish forms. The total average phytoplankton abundance was 419,414 unit/L. Few species were responsible for the main bulk of phytoplankton namely Merismopedia tenuissima, Cylindrotheca closterium, Cyclotella sp., Skeletonema costatum, Scenedesmus quadricauda, Scenedesmus bijugus, and Tetradesmus dimorphus. During the study period, El-Mex Bay was affected by the presence of 13 harmful and /or toxic algal species, among which the mediophyte species Skeletonema costatum was responsible for the peak occurring during autumn (2018). The results of the recorded nutrients indicated that the Bay is highly loaded, where NH4, NO2, NO3, PO4, and SiO4 attained 141.68 µM, 25.61 µM, 151.16 µM, 10.73 µM, and 232.86 µM, respectively. The macroalgal flora was represented only by the two opportunistic species (Ulva fasciata and Ulva intestinalis). Both species could survive in freshwater conditions exhibiting very broad salinity tolerance (6.51–38.41‰) and a high level of nitrogenous compounds. Those results revealed that El-Mex Bay suffers from pollution and deterioration of water quality.