Macrophytes and phytoplankton including cyanobacteria are main primary producers in aquatic environments. Macrophytes can maintain water quality by suppressing phytoplankton growth through a number of mechanisms: while e.g. the absorption of high amounts of nutrients and the provision of refuge from predation for herbivorous aquatic fauna are widely accepted macrophyte functions, the role of their release of allelopathic substances in suppressing phytoplankton is increasingly being studied. Some macrophyte species can support the growth of epiphytic cyanobacteria providing them an advantage over planktonic species in the competition for nutrients. On the other hand, some cyanobacteria dominate in eutrophic water bodies and produce cyanotoxins that exert allelopathic substances which may contribute to the decline of macrophytes. Macrophytes can interact with these cyanotoxins in different ways including bioaccumulation and biotransformation. This review focuses on such allelopathic interactions between macrophytes and toxic cyanobacteria. The article also suggests methods for researchers and water resources managers for the application of macrophytes to control harmful cyanobacterial blooms and as phytoremediators for toxin elimination from water bodies.