Fishes are affected by the bacterial load and species present in the surrounding area. Therefore, bacterial load on/in fishes can be used as an indicator of aquatic pollution. Bacterial load was estimated in fish tissues of different tilapia species (Oreochromis niloticus,  Sarotherodon  galilaeus, and Tilapia  zilli) collected from the entrance and middle El-Ramla and Abu Simbel Khors. Results indicated that fishes of Abu Simbel Khor recorded higher bacterial loads than those of El-Ramla Khor, also fishes of entrance khors recorded higher bacterial loads than the middle. Salmonella sp. and Escherichia coli were detected in fish samples collected from Abu Simbel Khor more than in fishes collected from El Ramla Khor. Vibrio chorella was detected in fish samples collected from El Ramla Khor more than those collected from Abu Simbel Khor. The results reflect the exposure of Lake Nasser Khors to various pollutions, especially in its southern part. Here, it is necessary to follow up fishing and tourism boats, also coastal farms around the Khors, to reduce or prevent the causes of pollution of Lake Nasser and its Khors.