In Egypt, Lake Nasser is an important water resource. So, this study was concerned with evaluating the quality of the lake via determination of bacterial load in sediment samples collected from fifteen sites along the lake, and ten sites of Dahmit and Tushka Khors before and after flooding in the years 2016 and 2019. Results indicated that the highest bacterial density was recorded during drought season and lowest in flooding seasons of both years. Statistically, the highest bacterial load was recorded in the middle stream compared to the other two sides. The northern part of Lake Nasser recorded higher bacterial density in 2019, while the southern part recorded higher bacterial density in 2016. Salmonella spp < em>. were detected in about 56% of Lake Nasser samples in 2016, compared to 33% in 2019. Also, year 2016 recorded higher bacterial densities than in 2019, this may be due to the difference in flood strength, lake level, and sedimentation capacity from year to another. Finally, it is important to constantly monitor the quality of Lake Nasser to avoid any alteration of its natural characteristics.