Benthic macroinvertebrates and zooplankton play crucial roles in trophic dynamics and serve as indicators of environmental changes in river ecosystems. This study examined the spatial and temporal distribution of these organisms in the main channel of Lake Nasser and its khores, Khor El-Ramla and Khor Dahab, during pre-flood and post-flood phases. Zooplankton communities included Copepoda, Cladocera, and Rotifera, with Copepoda dominating in the main channel and Khor El-Ramla. In Khor Dahab, Copepoda thrived post-flood, while Cladocera were more prevalent pre-flood. Common zooplankton species included Thermodiaptomus galebi, Thermocyclops sp., and Brachionus sp. Macrobenthic invertebrates from Annelida, Arthropoda, Mollusca, Nematoda, and Cnidaria were also identified, with Annelida and Arthropoda being dominant in the main channel. In the khores, Mollusca and Arthropoda made up significant portions of the benthic community. Key species included Limnodrilus udekemianus and Melanoides tuberculata. Hierarchical cluster analysis revealed that Khor Dahab had distinct physical and biological characteristics compared to Khor El-Ramla and the main channel. Post-flood, transparency, depth, electrical conductivity, and pH were the main factors affecting zooplankton and macrobenthos, while pre-flood conditions were influenced by depth, dissolved oxygen, and temperature.