Blooms of the cyanobacterium Microcystis threaten aquatic ecosystems. Protozoa grazing can control unicellular Microcystis populations; however, Microcystis blooms are composed of multicellular colonies that are thought to prevent grazing. We show that this is not so: the model ciliate Paramecium has an impact on Microcystis populations through grazing, even when large colonies occur, and this leads to a corresponding decrease in toxic microcystins. Notably, as the number of large colonies increased, Paramecium exerted top-down control by altering its feeding behavior: once the colony size was >12-20 μm, Paramecium no longer acted as a "filter feeder"; instead, it became a "surface browser," grazing around and between larger colonies, removing individual Microcystis and small colonies. However, as the proportion of large colonies increased, exponentially reducing the surface area to volume ratio, the impact of Paramecium decreased exponentially. This study provides new insights into how protozoa may affect Microcystis populations through top-down control of blooms.