With the rapid advancement of nanotechnology and its widespread applications, increasing amounts of manufactured and natural nanoparticles (NPs) have been tested for their potential utilization in treating harmful cyanobacterial blooms (HCBs). NPs can be used as a photocatalyst, algaecide, adsorbent, flocculant, or coagulant. The primary mechanisms explored for NPs to mitigate HCBs include photocatalysis, metal ion-induced cytotoxicity, physical disruption of the cell membrane, light-shielding, flocculation/coagulation/sedimentation of cyanobacterial cells, and the removal of phosphorus (P) and cyanotoxins from bloom water by adsorption. As an emerging and promising chemical/physical approach for HCB mitigation, versatile NP-based technologies offer great advantages, such as being environmentally benign, cost-effective, highly efficient, recyclable, and adaptable. The challenges we face include cost reduction, scalability, and impacts on non-target species co-inhabiting in the same environment. Further efforts are required to scale up to real-world operations through developing more efficient, recoverable, reusable, and deployable NP-based lattices or materials that are adaptable to bloom events in different water bodies of different sizes, such as reservoirs, lakes, rivers, and marine environments.