Macrophytes play a significant role in shaping plankton communities by shading, controlling water turbulence, and nutrient availability, while also producing allelochemicals causing varying effects on different organisms. Many researchers have shown that when live macrophytes are present, they inhibit cyanobacteria. However, their widespread use is often limited due to numerous concerns, including invasive characteristics. This study focused on the applicability of Egeria densa extracts to suppress Microcystis aeruginosa. We employed pure water and dimethyl sulfoxide, to obtain compounds from E. densa. The results revealed that E. densa aqueous extracts stimulated M. aeruginosa growth, whereas organic extracts exhibited suppression. Specifically, at low concentrations of organics extracts (0.5 and 1 g/L), after day 4, the growth inhibition was confirmed by significantly higher (p < 0.05) stress levels shown in cells treated with low concentrations. The highest inhibition rate of 32% was observed at 0.5 g/L. However, high concentrations of organic extracts (3 and 6 g/L), showed increased growth compared with control. These results suggest that high concentrations of organic extracts from E. densa potentially suppress allelochemical-induced M. aeruginosa inhibition due to high nutrient availability. In comparison with an aqueous solvent, the use of organic solvent seems to be more effective in efficiently extracting allelochemicals from E. densa.