Lake Nasser plays a fundamental role in both local and national economy. Phyto-plankton represents one of the most interesting groups in water habitats and aquatic food chains. The present work aimed to estimate the spatiotemporal variation in phytoplankton structure, biovolume and carbon content in Khor Ramla and Khor Abu-Simbel of Lake Nasser; during the highest water level in early autumn and the lowest water level in late spring. Nine stations along each khor have been studied in 2014. A total of 180 phytoplankton taxa related to four algal divisions were identified. These divisions are: Chlorophyta (94 taxa), Cyanophyta (52 taxa), Bacillariophyta (32 taxa) and Dinophyta (2 taxa). Microcystis comperei, M. aeruginosaand Lyngbya limnetica were the dominant cyanophytes. Cosmarium spp.,Coelastrum reticulatum, Oocystis borgei, Eutetramorus fottii, Ankistrodesmus spiralis, Pediastrum simplex, Euastrum sp. andDictyosphaerium pulchellum represented the most abundant species of chlorophytes. Diatoms were dominated mainly by Aulacoseira granulata, A. ambigua, A. muzzanensis, Cyclotella ocellata, C. glomerata and Cymbella affinis.In spring, the average total biovolume of Khor Abu-Simbel (81.63 mm³/l) was higher than that of Khor Ramla (1.94 mm³/l). In autumn, the average total biovolumes in Khor Ramla (3.65 mm³/l) and Khor Abu-Simbel (3.09 mm³/l) were slightly different. Cyanophyta was dominant in both studied khors along the study period with obvious blooming at all stations of Khor Abu-Simbel during spring. In Khor Abu-Simbel, the carbon content of all groups during spring was higher than that of autumn, except for diatoms. In Khor Ramla, the carbon content of cyanobacteria and diatoms increased in autumn, while in Dinophyta and Chlorophyta the values increased in spring. A detailed discussion of the factors lead to the dominance and blooming of cyanobacteria in Lake Nasser was given. Canonical Correspondence Analysis (CCA) clarified that a combination of physical, chemical and biological factors rather than a single factor acted in harmony to control the composition and dynamics of phytoplankton community in Khor Abu- Simbel and Khor Ramla in Lake Nasser.