According to current paradigms, plant polyphenols control and structure planktonic phototroph communities in freshwater ecosystems. If released from macrophytes, they apparently stabilize the clear macrophyte-dominated state of shallow lakes. In addition, they are applied to combat nuisance blooms of phototrophs (mainly cyanobacteria) in small eutrophic lakes. However, contrasting results concerning the success both in field and laboratory studies, particularly when upscaling from laboratory to field effects, lead to the assumption that the effects of polyphenols are over-rated and certain mechanisms have been overlooked. Hence, we address four ecochemical and physiological issue matters: (1) Polyphenols undergo autocondensation at pH > 7; many field studies, however, are conducted at pH > 8.3 and it is therefore questionable whether polyphenols can have a sustainable control on the phototrophs. (2) The physiological state of the phototrophs under study, such as CO 2 supply, is seldom evaluated. If the phototrophs are optimally supplied with CO 2 , either much higher EC50 or even no effects were observed with identical species studied. (3) Polyphenols account only for one part of the observed allelochemical impact of macrophytes on planktonic phototrophs; further xenobiotics, such as alkaloids or fatty acids, might similary contribute. (4) Microcystis aeruginosa , the most common bloom-forming cyanobacterium, responds in at least three modes of action: oxidative stress and subsequent reduction of photosynthesis, blocking of the photosynthetic electron chain, and interference within heterotrophic processes. Understanding the modes of toxic action upon challenges by specific allelochemicals provides the platform for improvements of applied xenobiotics alone or in mixtures. Hence, the specific modes of action are worth deciphering rather than extending the existing catalog of phenotypic effect descriptions with often unrealistic high concentrations applied.