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Harmful algal blooms (HABs) in lakes and estuaries, caused by cyanobacteria, pose various threats to humans and the environment. Cyanobacteria produce microcystins (MCs) that make animals and people sick. Once airborne, cyanobacterial aerosols are rapidly transformed through heterogeneous reactions with atmospheric oxidants, which tend to occur much faster in air than in water. The important aspects of these transformations include the degradation of MCs and the production of reactive oxygen species (ROS) from oxidized organic matter (OM) in cyanobacterial aerosol. In this study, MCs in aerosols and water samples, collected in lakes (Lake Okeechobee, Georges Lake, and Doctors Lake) of Florida during HABs, were measured using enzyme-linked immunosorbent assay kits. Organic hydroperoxides (OHP) and the oxidative potential (OP) associated with aerosols collected at Doctors Lake were measured with 4-nitrophenylboronic acid and dithiothreitol assays, respectively. The decay of MCs and the evolution of ROS in cyanobacterial aerosols were also demonstrated in an outdoor chamber under ambient sunlight. MC concentrations (0.4–2.1 μg/L) during HAB periods were higher than the US EPA guideline (0.3 μg/L for pre-school age and 1.6 μg/L for school-age and above). Airborne MC concentrations ranged from 0.2 to 5.7 ng/m3. Regulations for airborne MC concentrations are yet to be established. In both field and chamber data, MCs decomposed but ROS substantially increased as aerosols atmospherically oxidized. Aerosolized OM concentrations during HABs were higher than those in dormant periods. OM in cyanobacterial aerosols was enriched at estuary Doctors Lake with high inorganic salt concentrations due to salting-out of water-soluble organics into lake-surface layers. Aerosolized OM concentrations were positively corelated to OP and OHP (r = 0.96 and 0.85, respectively) at Doctors Lake suggesting that cyanobacterial aerosols might adversely influence respiratory health. The longitudinal health impacts of aerosolized cyanobacteria emitted from HABs should be investigated in the future.