Mex Bay, west of Alexandria (Egypt) is a large, shallow and turbid coastal plain estuary of socio-economic importance. Along its salinity gradient (3.30 to 39.64), seven sampling stations were chosen to cover the different
habitats. Regionally, four water masses could be defined; the Mediterranean water mass of salinity >38.5, mixed Mediterranean of 30 to 38.5, diluted of 10 to 30 and drain water mass of salinity <10. Phytoplankton species were grouped into three major types: freshwater, coastal low salinity and euryhaline species. A massive spring bloom characterized the annual production cycle and attributed to Skeletonema costatum. Salinity shares in shaping the structure of diatomdominated communities, and its levels between 30 and 35 seem suitable ecological condition for their growth. A boundary of salinity 3.3-5.1 identified as a critical region for certain freshwater species, mostly cyanophytes.
Dinoflagellates existed with salinity above 14.8. Chlorophyll a (average 14.39 μg l-1) reached its maximum in mid summer. Chlorophyll a for cells <20 μm contributed over 65% of the biomass. During the phytoplankton blooms, the >
20 μm cells dominated (62.73% of total Chl. a) in May, both fraction size (50.1% and 49.9%, respectively) in July, and the <20 μm cells in September (67.52 %). No significant correlation was found between any chlorophyll a size
fraction and abundances of diatoms, euglenophytes, chlorophytes, and cyanophytes, except for the >20 μm size with dinoflagellate abundances. The distribution patterns of biomass showed relatively high Chl. a (average 15.68 μg
l-1, 83.73% <20 μm) at salinity <10; 26.24 μg l-1, 58.76 % <20 μm at salinity 10-30; and decreased values (6.16 μg l-1, 58.5 % <20 μm) and 0.99 μg l-1, 66.06%  <20 μm at salinity between 30-38.5, and > 38.5, respectively.
Values of the diversity index fluctuated between 0.34 nats (May) and 2.24 nats (September), linked with species diversity and blooming.