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Eutrophication and enhanced external nutrient loading of lakes and seas are most clearly reflected by increased cyanobacterial blooms, which are often toxic. Freshwater cyanobacteria produce a number of bioactive secondary metabolites, some of which have allelopathic properties, significantly influencing the biological processes of other algae, thereby affecting species composition and succession of the phytoplankton. The goal of this work was to investigate the influence of bloom-forming cyanobacterial exudates on the photophysiology of the green alga
Scenedesmus quadricauda
by chlorophyll fluorescence analysis. We were able to prove the effect of algal cell-free fltrates on the performance of
S. quadricauda
and demonstrate for the first time that the freshwater picocyanobacterium
Cyanobium gracile
has strong negative impact on the coexisting green alga. Neither the cyanotoxin (MYC, CYN and ATX) producing, nor the non-toxic strains showed any systematic effect on the production of
S. quadricauda
. Various strains of the cyanobacterium
Cylindrospermopsis raciborskii
inhibited the performance of the green alga independently of their origin. Our results urge further studies for a better understanding of the factors affecting the release of allelopathic compounds and the mechanisms of their effects on target organisms.