Harmful algal bloom (HAB) has become a recurrent event in the freshwater system, posing a great threat to ecosystem, human health, and economy. The purpose of this study was to investigate the effectiveness of quantitative polymerase chain reaction (qPCR) as an early monitoring tool of HABs, and then to mitigate HABs present at the Campus Lake of Southern Illinois University Carbondale by lab synthesized γFe2O3/TiO2 nanocomposite. In the first study, qPCR was utilized to determine gene copies of toxigenic bacterial species: mcyE for microcystin producers, rpoC for Cylindrospermopsis raciborskii and sxtA for saxitoxin producers in algal blooms from June to October 2021, the results were compared with the conventional monitoring methods: determination of Chl-a and phosphorus (dissolved phosphorus, DP) concentration. At the Campus Lake, C. raciborskii was not detected in any of the water samples, while mcyE was dominant (~51.2%) in the bloom during its peak bloom period in September. qPCR results indicated that it can quantify toxigenic cyanobacterial species at the early stage of bloom development and was more efficient and sensitive than Chl-a and DP determination. In the second study, synthesized γFe2O3/TiO2 nanocomposite was used to mitigate algal blooms by means of (i) inactivation of toxigenic cyanobacteria, (ii) photo-catalytic degradation of released cyanotoxins, and (iii) adsorption of nutrient phosphorus from water samples. γFe2O3/TiO2 nanocomposite inactivated toxigenic Microcystis aeruginosa and C. raciborskii cyanobacterial cultures by 95% and 90%, respectively, after 1 h interaction under simulated solar light. In the lake water samples, 88% inactivation of microcystin producing cyanobacteria was achieved by the nanocomposite. Natural organic matter (NOM) at final concentration of 75 mg/L DOC, slightly inhibited (~19% for 16S rRNA and ~23% for mcyE) the performance of the nanoparticles. Microcystin (MC-LR) and cylindrospermopsin (CYN) cyanotoxins in deionized water were removed by ~52% and ~46%, respectively, after 1 h interaction with γFe2O3/TiO2 under LZC-VIS (mostly visible) light. Additionally, γFe2O3/TiO2 nanocomposite was used as an adsorbent of nutrient phosphorus. Around 24% phosphorus was adsorbed after 3 h by the nanocomposite from lake water samples. Phosphorus adsorption by the nanocomposite was greatly reduced by NOM and bicarbonate ions. In comparison, effect of chloride ions on phosphorus removal was negligible. In summary, the lab fabricated γFe2O3/TiO2 nanocomposite can be potentially employed in HAB mitigation under solar light irradiation. The early monitoring and mitigation strategies developed in this study can help control the HABs for protecting public health and the ecosystems