Autogenous and allogenous control of the phytoplankton standing crop and biomass was proved in Mex Bay, west of Alexandria (Egypt). Among the clear signs of eutrophication are the heavy visible blooms, which became regular events, at intermittent periods during the warm seasons. The causative organisms progressed differently, the dinoflagellate, Gymnodinium catenatum, is well known toxic species. The Environmental Impact Assessment model (EIA) was applied to Mex Bay. It is a three-dimensional water quality and flow model, based on the three interacted dimensional: longitude, latitude and depth, calculations of time and space variations. The model deals with processes that affecting the water quality. It was initiated with measured field data and load input. The model was used to simulate phytoplankton biomass transport and ambient nutrient concentrations (nitrate, phosphate & ammonia). The model results and the field measurements are compared in order to fit the model. Generally, the calculated flow and concentrations corresponded well with observations. Deviations are attributed to several reasons. A notable influence of the main outfall on the concentrations, particularly in the near shore area, as well as, on the seawater quality was detected. The spatial distribution of the phytoplankton standing crop coincided clearly with the accompanied chlorophyll a concentrations calculated by the model. The results stressed the need to reduce load input into Mex Bay, in order to counteract eutrophication in Alexandria waters. Nitrogen reduction is more important for the whole area, while phosphorous reduction is more effective in the bay.