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Cyanobacterial blooms and their corresponding toxins are a major concern to human health when surface waters of eutrophicated lakes are the only source for drinking water supply. The aim of the study was to test effective methods for cyanotoxin elimination by using the bioaccumulation potential of aquatic macrophytes in order to reduce microcystin LR (MC-LR) concentrations from raw lake surface water before entering the drinking water plant for further processing. Laboratory assays with aquatic macrophytes were performed in order to assess the most favorable species and optimal biomass for cyanotoxin elimination, where Lemna sp., Myriophyllum sp., and Hydrilla sp. were shown to be the most efficient macrophytes. In a second phase a pilot scale pond system (e.g. replica of the outdoor pond system) was constructed to assess the toxin elimination efficiency of 5.0 g L(-1) biomass of combined macrophytes. The applied macrophytic biomass reduced an initial MC-LR concentration of 12.1 and 9.2 microg L(-1) to values below the WHO guidelines for drinking water of 1.0 microg L(-1) (MC-LR) in only three days. Applying these results in a specially constructed outdoor pond system resulted in > 84% of toxin elimination at an initial concentration of 1.1 microg L(-1) MC-LR within the raw lake water.