The distributions of major phytoplankton groups were quantified to estimate the relative contribution of different groups to spatiotemporal dynamics in the northern part of Damietta branch, River Nile, Egypt, in response to a complex of physical and chemical conditions. The study was based on seasonal sampling over one year (summer 2015 to spring 2016) conducted at 6 freshwater and 6 marine sites. Limnological parameters, including electrical conductivity, alkalinity, orthophosphate, reactive silicate, nitrite, nitrate and ammonium, were simultaneously measured to determine the possible factors affecting the phytoplankton composition. Individuals within each phytoplankton groups were expressed as count (×10⁵) per liter. Distinct variations in EC were detected between fresh and estuary habitats, however, other parameters shown spatiotemporal fluctuations. The phytoplankton communities were dominated by five common groups including Bacillariophyta, dominant in both habitats, Chlorophyta and Cyanophyta dominant in freshwater, Pyrrophyta and Euglenophyta dominant in estuary, different abundance contributions were detected between groups depending on seasons and sites. Thus, in River Nile, a complex of physical, chemical and biological factors that affected by natural and anthropogenic activities is responsible for the ecological determinants of the phytoplankton population.