Lake Nasser is a reservoir of freshwater for drinking and irrigation in Egypt and it constitutes an important share in the fisheries sector. This study aims to acquire a better understanding of the status of phytoplankton distribution in Lake Nasser under the current flood regime and before the construction of the Grand Ethiopian Renaissance Dam (GERD). Samples were collected from fifteen sites representing different lake sectors along the main channel of the lake during 2016−2017. Approximately 103 species were recorded, belonging to six different classes, dominated by Cyanobacteria, Bacillariophyceae, Chlorophyceae, whereas Euglenophyceae, Dinophyceae and Chrysophyceae were rare. Based on the abundance of phytoplankton species, the pre-flood and post-flood seasons were very well discriminated. A major blooming of Cyanobacteria in the Tushka sector was detected during the pre-flood season, whereas this phenomenon diminished in the post-flood period when Bacillariophyceae and Chlorophyceae appeared. The results of this study indicated that the most important factors affecting phytoplankton species distribution during pre-flood and post-flood seasons are temperature, nutrients and total dissolved solids. The study confirms that flood regime substantially affects the phytoplankton abundance and distribution in Lake Nasser.