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Increased proliferation of algae is a current problem in natural and artificial water bodies. Controlling nutrients is the most sustainable treatment of increased algal proliferation, however in certain cases, it is not sufficiently available, or it does not provide results fast enough. Chemicals derived from natural sources, which could be effective in low concentrations and are biodegradable, may have an advantage over conventional chemical treatments. The main aim of the present study was to investigate the anti-cyanobacterial and anti-algal properties of allyl-isothiocyanate-containing essential oil produced from horseradish roots with a complex approach of the topic: on laboratory strains of cyanobacteria and eukaryotic algae, on microcosms containing natural phytoplankton assemblages, and on semi-natural biofilms. The results show that acute treatment can significantly reduce the viability of all the tested cyanobacteria and eukaryotic algae. Results of microcosm experiments with natural phytoplankton assemblages show that horseradish essential oil from 7.1 × 10−6% (v/v) is applicable to push back phytoplankton proliferation even in natural assemblages. The individual number in the biofilm was dropped down to one-fifth of the original individual number, so 7.1 × 10−6% (v/v) and higher concentration of the essential oil can be considered as a successful treatment against biofouling.