Coagulation followed by floc separation is a key process for the removal of algal organic matter (AOM) in water treatment. Besides optimizing coagulation parameters, knowledge of the properties of AOM-flocs is essential to maximizing AOM removal. However, the impact of AOM on the floc properties remains unclear. This study investigated how peptides/proteins derived from the cellular organic matter (COM) of the cyanobacterium Microcystis aeruginosa influenced the size, structure, and shape of flocs formed at different shear rates (G). Flocs formed by kaolinite, COM-peptides/proteins and a mixture of the same were studied, and the effect of intermolecular interactions between floc components on floc properties was assessed. The coagulation experiments were performed in a Taylor-Couette reactor, with aluminum (Al) or ferric sulphate (Fe) utilized as coagulants. Image analysis was performed to gauge floc size and obtain data on fractal dimension. It was found that floc properties were affected by the presence of the COM-peptides/proteins and the coagulant used. COM-peptides/proteins increased floc size and porosity and widened floc size distributions. The Fe coagulant produced larger and less compact flocs than Al coagulant. Moreover, the decrease in floc size that occurred in parallel with increase in shear rate was not smooth in progress. A rapid change for the kaolinite-coagulant suspension and two rapid changes for the suspensions containing COM were observed. These were attributed to various intermolecular interactions between floc components participating in coagulation at different G. Based on the results obtained, shear rates suitable for efficient separation of flocs containing COM were suggested.