Harmful and toxic cyanobacterial blooms in freshwater constitute critical environmental problems and are becoming more frequent as a consequence of global climate change. One mitigation strategy is flocculation, which could be achieved with treatment by highly efficient, non-toxic, and biodegradable agents. Here, we report two amphiphilic peptide dendrimers (AmPDs), KK2 and KK2K4, for the removal of the toxic and bloom-forming cyanobacterium Microcystis aeruginosa from freshwater. KK2 and KK2K4 are composed of a hydrophobic alkyl chain and a positively charged polylysine dendron of the first and second generation, respectively. Owing to electrostatic interactions with the negatively charged cell surface of M. aeruginosa, KK2 and KK2K4 could quickly capture the cyanobacterial cell population via flocculation at very low concentrations. When combined with the natural clay sepiolite, the two AmPDs were even more efficient in promoting cell flocculation. The most performant system, with 3.0 mg/L KK2K4 and sepiolite clay, could remove 97.1 % of M. aeruginosa within 15 min by forming stable flocs. Remarkably, such a system was able to trap toxin molecules released by cyanobacterial cells, thus limiting its destructive impact on ecosystems. This study demonstrates how self-assembling dendrimer materials can resolve cyanobacterial blooms, providing an innovative solution to this environmental challenge