A major task for categorizing an ecological flood is establishing the effects of environmental enrichment on nutrient availability, which may affect phytoplankton species composition and internal biochemical contents. The current study seeks to analyze the interaction between environmental variables, phytoplankton composition, and its internal biochemical content during the flood season at Lake Nasser, Egypt. Samples were collected from four water depths (surface, 10 m., 20 m., and bottom) at five sites along the main channel of Lake Nasser during the flood season in August 2017. A major bloom of Cyanobacteria was detected along with retardation of biopolymeric particulate organic carbon availability. Principle component analysis indicated that the most significant parameters affecting total phytoplankton distribution, especially Cyanobacteria, were temperature, dissolved oxygen, nitrite, and phosphate. Moreover, a negative correlation was reported between protein content, organic carbon and total biochemical content with nitrate. The highest biopolymeric particulate organic carbon value (37.15 mg/l), protein (88.64 mg/l) and lipid contents (1.5 mg/l), were recorded at El-Madiq site with total biochemical content of 91.29 mg/l and associated optimum nutrient levels. This interpreted with an increase of Chlorophycean species biomass (812.5 × 10³ cell l^-1). Flood causes an elevation in the minor lipid cellular composition more than carbohydrates at all sites. Flooding in Lake Nasser altered its water quality by introducing oxygen and nutrients, along with changes in phytoplankton species composition and internal biochemical content.