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Harmful cyanobacterial blooms (HCBs) are becoming a major challenge for the management of both natural and man-made freshwater lakes and reservoirs. Phytoplankton communities are an essential component of aquatic ecosystems, providing the basis for natural food webs as well as important environmental services. HCBs, driven by a combination of environmental pollution and rising global temperatures, destabilize phytoplankton communities with major impacts on aquatic ecology and trophic interactions. Application of currently available algaecides generally results in unselective elimination of phytoplankton species, disrupting water ecology and environmental services provided by beneficial algae. There is thus a need for selective cyanocidal compounds that can eliminate cyanobacteria while preserving algal members of the phytoplankton community. Here, we demonstrate the efficacy of N-halamine derivatized nanoparticles (Cl NPs) in selectively eliminating cyanobacteria, including the universal bloom-forming species Microcystis aeruginosa , while having minimal effect on co-occurring algal species. We further support these results with the use a simple microfluidic platform in combination with advanced live-imaging microscopy to study the effects of Cl NPs on both laboratory cultures and natural populations of cyanobacteria and algae at single cell resolutions. We note that the Cl NPs used in this work were made of polymethacrylamide, a nonbiodegradable polymer that may be unsuitable for use as a cyanocide in open aquatic environments. Nevertheless, the demonstrated selective action of these Cl NPs suggests a potential for developing alternative, biodegradable carriers with similar properties as future cyanocidal agents that will enable selective elimination of HCBs.