Aquatic macrophytes are plants that live in water or wet soil, grow profusely in lakes and waterways, and provide several ecological benefits. Lake Nasser, an artificial reservoir, has been the most critical element in Egypt’s social and economic development. The temperature changes and the Ethiopian Renaissance Dam represent the most prominent challenge that poses the greatest threat to the Lake’s water. Intense disturbance in aquatic macrophytes, caused by the very large fluctuation in water level and temperature was observed. Currently, only three submerged macrophyte species (Myriophyllum spicatum, Potamogeton schweinfurthii and Najas marina) were detected at Lake Nasser. The composition and structure of the submerged macrophytes community had a pronounced impact on fish production and diversity in the Lake. As the Lake is located in the subtropical region, where warm water fosters plant growth, the dangers of some macrophytes may be high. Therefore, additional studies are needed to avoid the negative effects of climate change and the impact of the Renaissance Dam on Lake Nasser and to optimize the most benefit of its aquatic macrophytes.