The Nile River is exclusively Egypt's freshwater supply and is used to cool steam turbines in power plants, most of which are located along its course. An investigation was conducted to address the water quality in six areas affected by thermal discharge along the Nile and to monitor the potential effects of temperature fluctuations on the biodiversity of bacteria, phytoplankton, and zooplankton communities. Samples were collected from the upstream, downstream, and discharge zones of each power plant. Temperatures increased more at the mixing points than in the upstream and downstream locations, while transparency and dissolved oxygen levels were the lowest at the mixing points. The water quality index for the Nile ranged from 68 (medium) to 93 (excellent), with the lowest values found near the thermal discharge points. Fecal coliform and fecal streptococci counts ranged from 3 to 1100 and 3 to 1200 MPN/100 ml, respectively, with the mixing points showing the lowest levels of pollution-related bacterial markers. Our results indicate that plankton abundance and dominance were influenced by temperature at the mixing points. Seasonal changes in zooplankton composition and density were observed, with rotifers consistently being the dominant group. It is recommended to regularly monitor the condition of the Nile water, especially after the completion of the Grand Ethiopian Renaissance Dam and the decrease in Egypt's share of the Nile water, as these changes could lead to increased water temperatures near the power plants.