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Due to the climate change and human activity, the frequency and intensity of algal blooms have increased significantly. Recent studies have shown that during the bloom event, evaluated levels of cyanobacteria could infiltrate the drinking water treatment process and emerge in the filtered and disinfected water, thus threatening the safety of the drinking water supply. Among these concerned cyanobacteria, Microcystis aeruginosa is one of the most commonly detected species that cause algal bloom in a fresh water body. The present work was designed to investigate the transport and retention behaviour of Microcystis aeruginosa in a packed column to resolve the mechanisms that drive the transport behaviour of Microcystis under various operational conditions. The results showed that lab cultured Microcystis aeruginosa could effectively break through the packed column regardless of ionic strength, media size or flow rate, as well as the presence of dissolved organic matter in the water under the conditions investigated. Such behaviour significantly contradicts those of fluorescent microspheres, which are commonly considered as ideal colloids. In addition, the combined impacts of pre-oxidation technologies and filtration on Microcystis aeruginosa removal were tested systematically. It was found that even the cells have been lysed/oxidized, no significant improvement of cell removals were observed in packed column. This paper provides a significant and comprehensive record of transport and retention behaviour of Microcystis aeruginosa in porous media. The results found herein suggest that in addition to the effort preventing toxin release/exposure during bloom events in source water, engineers and researchers should also pay attention to the transport and retention of Microcystis aeruginosa and other algal cells in filters to minimize the risk of breakthrough of cyanobacteria cells in the drinking water treatment process. (C) 2019 Elsevier Ltd. All rights reserved.