Abstract: Background and Objective: Phytoplankton and macroinvertebrates are two of the most interesting groups in freshwater habitat and aquatic food chains. The objective was to study phytoplankton and macroinvertebrates associated with aquatic macrophyte Myriophyllum spicatum (M. spicatum) at Dahmeit and Tushka West khors of Lake Nasser during flood cycle (before, during and after flood). Materials and Methods: About 1.0 L Ruttner Sampler was used to collect composite surface water samples for studying phytoplankton. Macrophyte, Myriophyllum spicatum was collected from the same sites at the same times. The associated macroinvertebrates were separated with a net 500 μm for identification and the macrophyte was dried and weighed. Correlation analysis between the measured parameters of water, phytoplankton and macroinvertebrates associated with Myriophyllum spicatum were carried out using Statgraphics program. Results: The dominant groups of phytoplankton were Cyanophyta, Chlorophyta and Bacillariophyta while, Oligochaeta, Hirudinea, Crustacea, Insecta and Gastropoda were the dominant groups of macroinvertebrates associated with Myriophyllum spicatum. The highest densities of phytoplankton were recorded after flood (8.16×106 and 1.27×107 cells L–1 at Dahmeit and Tushka khors, respectively). Meanwhile, the highest densities of associated macroinvertebrates were recorded during flood (576 and 690 organisms/100 g plant dry wt at Dahmeit and Tushka khors, respectively). The most dominant macroinvertebrate taxa were Pristina sp., Bulinus truncatus, Gyraulus ehrenbergi and Chironomid larvae while those of phytoplankton were Chroococcus spp., Pseudoanabaena sp., Ankistrodesmus falcatus, Dictyosphaerium pulchellum, Scenedesmus bijugatus and Aulacoseira granulata. The results of water quality index (WQI) and species diversity indicate the improvement of water quality in the study area by flood. Tushka West khor (upstream) was more productive in phytoplankton and associated macroinvertebrates than Dahmeit khor (downstream). Species evenness of macroinvertebrates shows negative significant correlation with species diversity (-0.6) and evenness (-0.5) of phytoplankton. Also, negative significant correlation (-0.76) was detected between species richness of phytoplankton and associated macroinvertebrates. Canonical correspondence analysis (CCA) shows that total count of phytoplankton was not affected by total count of associated macroinvertebrates and its groups. Conclusion: The flood cycle influenced microalgae and macroinvertebrate communities by stimulating spatial and seasonal variations of phytoplankton and invertebrates succession and density.