In recent years, there has been an increasing focus on the prospect of exploiting macrophytes as an alternative strategy to control undesired algal growth. The present research was conducted to study the effect of different concentrations of an aqueous stem extract of Persicaria salicifolia on the growth, some metabolites, and antioxidant enzymes of the green microalgae Synechocystis pevalekii and Tetradesmus bernardii. Chlorophyll a, dry weight, total protein, total carbohydrate, and proline contents of the tested algae decreased with increasing the crude extract concentrations of P. salicifolia. In general, catalase, superoxide dismutase, and lipoxygenase activity of T. bernardii increased with increasing the aqueous extract of P. salicifolia. The identification of phytochemical components of the plant extract by gas chromatography-mass spectrometry (GC-MS) revealed the presence of various biologically active compounds such as 11-Octadecenoic acid, methyl ester (18.03%) and 9,12-Octadecadienoic acid methyl ester (15.03%) that are capable of inhibiting the growth of S. pevalekii and T. bernardii. Therefore, P. salicifolia may provide a cheap and environmentally friendly alternative for controlling microalgae in aquatic ecosystems.