Microcystins are cyanobacterial toxins that are problematic for water authorities due to their resistance to conventional water treatment. Granular activated carbon (GAC) filtration has been shown to be effective in removing microcystin from water using both adsorption and biodegradation removal mechanisms; however, little is known regarding which removal mechanism predominates and to what extent. In this study, microcystin removal due to adsorption and biodegradation in GAC filtration were discriminated and assessed by commissioning three parallel laboratory columns, including a sterile GAC column, a conventional GAC column and a sand column. The results demonstrate that biodegradation is an efficient removal mechanism once it commences and that the rate of biodegradation was dependent upon temperature and initial bacterial concentration. Adsorption of microcystins was prevalent during the initial stages of the GAC columns and was modelled using the homogeneous surface diffusion model (HSDM). The HSDM provided evidence that an active biofilm present on the surface of the conventional GAC hindered adsorption of microcystin compared with the sterile GAC with no active biofilm. Up to 70% removal of microcystin-LR was still observed after 6 months of operation of the sterile GAC column, indicating that adsorption still played a vital role in the removal of this toxin.