One of the major challenges in reducing the risk of cyanobacteria to environmental health is employing safe and effective techniques to treat and remove their cells from water sources. Nano-materials such as copper oxide nanoparticles (CuO NPs) have drawn a lot of interest as a sustainable way to inactivate microorganisms and adsorb contaminants in wastewater because of their catalytic activity, low cost and low cytotoxicity. Herein, we investigated the inhibitory effects of undoped and cobalt-doped copper oxide nanoparticles (Co-CuO NPs) on Microcystis aeruginosa, a common toxic cyanobacterium found in water sources. The results showed that both undoped and Co-doped CuO NPs inactivated M. aeruginosa growth, with doped NPs having a higher effectiveness (100%) than undoped ones (99%) at 25 mg/L. According to regression Probit analysis, the medium effective concentrations (EC50) of these NPs varied with exposure time, reaching their lowest values (0.8 and 0.3 mg/L, respectively) at 96 hours and their greatest values (5.6 and 4.6 mg/L, respectively) at 24 hours. Additionally, the results showed that these NPs can concurrently adsorb microcystin (MC) toxins that are released into the medium upon cell lysis. Since nanoparticles are firmly bound to the surfaces of cyanobacterial cells, they settle as flocs and are easily eliminated with the sludge. Therefore, both undoped and doped CuO NPs could be employed as coagulants in drinking water treatment plants to remove microcystin toxins and cyanobacterial cells at the same time.