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Frequent outbreaks of harmful algal blooms (HABs) have brought adverse impacts on human health, economic viability, and recreational activities in many communities in the United States. Cyanobacteria (or blue‐green algae) blooms are the most common type of HABs in surface water. Current bactericides for controlling the blooms are disadvantageous due to the recycling difficulty. In this study, an innovative magnetic nanomaterial―γFe2O3/TiO2 nanoparticle—was used to inactivate toxic cyanobacteria species found in a lake in Southern Illinois that frequently experienced HABs. Cyanotoxin genes of mcy, nda, cyr, and sxt were used for targeting microcystin‐, nodularin‐, cylindrospermopsin‐, and saxitoxin‐producing cyanobacteria, respectively, by quantitative polymerase chain reaction (PCR) method. It was found that the concentration of chlorophyll a presents a strong correlation (R2 = 0.6024) with the gene copy obtained from 16S rRNA targeted for all cyanobacteria, but not with that from individual toxigenic cyanobacteria. The inactivation efficiencies of the nanomaterials under visible light were as high as 5‐log and 1‐log for cyanobacteria species containing mcyE/ndaF and sxtA genes, respectively, an improvement over the treatment under darkness. These nanomaterials can be recycled by their magnetic properties for reuse. Communities susceptible to HAB outbreaks are expected to benefit from the developed method for mitigating the blooms. Practitioner points: Lab‐made γFe2O3/TiO2 nanoparticles can be used to inactivate microcystin/nodularin‐ and saxitoxin‐producing cyanobacteria species.qPCR method can be used for targeting toxic cyanobacteria; Chl a cannot be used as a standalone indicator for HABs.Better inactivation efficiency under visible light indicated possible application of the technology under sunlight for HAB mitigation from surface water. [ABSTRACT FROM AUTHOR]