Submerged macrophytes play a significant role in stabilising clear water conditions in coastal wetlands, partly due to their interference with microalgal growth via allelopathy. One of our recent studies tested allelopathic effects of several macrophyte species on microalgae. This study was carried out with the charophytes Chara hispida, C. baltica, C. vulgaris and Nitella hyalina, and with the angiosperm Myriophyllum spicatum. A higher inhibitory effect on natural microalgal assemblages was measured when charophyte exudates were present, particularly in the case of C. hispida. When mixed exudates from several populations were used, the inhibitory effects on microalgal growth were even stronger. Thus, it is likely that in aquatic communities macrophytes cause synergistic allelopathic effects on other organisms. Based on our previous results, the hypothesis that arises is whether the polyphenols of different macrophyte species with allelopathic activity are complementary rather than redundant. This fact would explain that diverse macrophyte assemblages exert a greater negative effect on the microalgae growth. To test this hypothesis, tissues of the several macrophyte species cultivated in the laboratory in monocultures were analysed for polyphenols. The analytical procedure consisted of extractions (Solid Phase Extraction Strata X Cartridge), separation (Ultra‐high Performance Liquid Chromatography (UPLC)) and setting ranges and calibration curves of compounds. The polyphenols found in the target macrophytes were: Gallic Acid, Protocatechuic Acid, Protocatechuic Aldehyde, Catechin, pOH-Benzaldehyde, Epicatechin, pCoumaric Acid, Quercetin, Epigallocatechin Gallate, pOHBenzoic Acid, Kaempferol 3-glucoside, Quercetin 3-Glucoside, Quercetin 3-Rhamnoside, Ethyl Caffeate. The number of different polyphenols in macrophytes varied from six in the angiosperm to one in C. baltica. M. spicatum’s polyphenols were mainly of the flavonoid type. Benzenoic polyphenols were the most common in charophytes. A cluster analysis (Gower index and paired group method) of the macrophyte species based on the tissue polyphenol content (quantified as mg compound/Kg DW of plant) was performed. M. spicatum formed a monospecific group separated from charophytes, and Chara species grouped together separately from N. hyalina. Thus, a complementary allelopathic effect might be likely to occur in aquatic systems dominated by dense and diverse stands of submerged vegetation.