In recent years macrophytes are being considered promising tools in the biocontrol of harmful cyanobacteria blooms (cyanoHABs). In this study, the inhibitory effect of aqueous extracts of Ranunculus aquatilis and Nasturtium officinale on Microcystis aeruginosa growth was assessed via six treatments (0%, 0.1%, 0.25%, 0.50%, 0.75%, and 1% extracts). Chlorophyll a and carotenoid content were analyzed and changes in cell and colonial morphology of M. aeruginosa cultures were observed. Also, to reveal potential allelochemical compounds, total phenols (TPs), total flavonoids (TFs), and tannins (TTs) were analyzed in both extracts. The obtained results showed that M. aeruginosa growth was significantly inhibited by R. aquatilis and N. officinale aqueous extracts in a concentration-dependent way. After 8 days of treatment, the highest inhibition rates reached 100% and 75.74% respectively. The Chlorophyll a and carotenoid concentrations were decreased compared to the control group. Colonial and cell and colonial morphology changes were observed under the treatment group with 1% of aqueous extract accompanied by sedimentation of the cyanobacterial cells. This study shows that M. aeruginosa growth inhibition was induced by the total polyphenol, flavonoids and tannins. It was concluded that theses macrophytes may control M. aeruginosa and may be useful to control harmful blooms in lake-reservoirs.