The current study addressed the variation in epiphytic algae's total protein and lipid contents, as well as bacteria, viz. total coliforms (TC), faecal coliforms (FC), and faecal streptococci (FS) in the aquatic ecosystem during winter and summer. In winter (after flooding), epiphytic algae with 179 species belonging to 6 algal groups were recorded in the five stations of Lake Nasser, Egypt. While in summer (before flooding), the total number of epiphytic algae decreased to 144 species belonging to 5 algal groups. Compared to the value of bacteria after flooding, TC, FC, and FS bacteria possessed greater values before flooding. The high number of those bacteria in water indicates the possibility of pathogen presence. The total protein content of epiphytic algae revealed a large temporal significant change (p ˂ 0.01) across seasons; whereas, total lipid showed a very large temporal significant difference (p ˂ 0.003). No variances were detected in the space between the stations. After flooding, the total lipid content of the epiphytes was positively affected by total coliform and faecal coliform bacteria (r = 0.81 & 0.65, respectively). The results proved that variable environmental conditions (after flooding & before flooding) and seasons, as well as the bacterial load of the water body, affect the epiphytes species and their biochemical composition and diversity in the aquatic ecosystem.