Natural leaf litter inputs is one factor that may help to minimize the likelihood of excessive algal growth. We tested the allelopathic effect of the grey willow (Salix atronicerea) on two phytoplankton species: Planktothrix agardhii (toxic and non-toxic cyanobacterial strains) and Scenedesmus communis (a chlorophyte). Effect was evaluated by combining leaf extracts and pulse amplitude modulation (PAM) chlorophyll fluorescence yield to measure photosynthetic activity responses. Phototrophic growth of the cyanobacterial species was suppressed even at very low concentrations of the extract while growth of the chlorophyte species was not affected. In the two cyanobacteria strains, inhibition of the chlorophyll fluorescence yields was significantly higher in the microcystin-free strain. Polyphenols are suspected to cause oxidative damage to cyanobacteria and thereby induce selective growth inhibition, similarly to hydrogen peroxide treatments against harmful cyanobacteria. Our results evidence willow extract or exudate as a promising agent selectively affecting cyanobacterial growth, but further studies are needed to determine the environmental impact and the inhibiting process. © 2016 Elsevier B.V.