In some lakes, large amounts of the potentially toxic cyanobacterium Microcystis overwinter in the sediment. This overwintering population might inoculate the water column in spring and promote the development of dense surface blooms of Microcystis during summer. In the Dutch Lake Volkerak, we found photochemically active Microcystis colonies in the sediment throughout the year. The most vital colonies originated from shallow sediments within the euphotic zone. We investigated whether recruitment of Microcystis colonies from the sediment to the water column was an active process, through production of gas vesicles or respiration of carbohydrate ballast. We calculated net buoyancy, as an indication of relative density, using the amounts and densities of the major cell constituents (carbohydrates, proteins, and gas vesicles). Carbohydrate content of benthic Microcystis cells was very low throughout the year. Buoyancy changes of benthic Microcystis were mostly a result of changes in gas vesicle volume. Before the summer bloom, net buoyancy and the amount of buoyant colonies in the sediment did not change. Therefore, recruitment of Microcystis from the sediment does not seem to be an active process regulated by internal buoyancy changes. Instead, our observations indicate that attachment of sediment particles to colonies plays an important part in the buoyancy state of benthic colonies. Therefore, we suggest that recruitment of Microcystis is more likely a passive process resulting from resuspension by wind-induced mixing or bioturbation. Consequently, shallow areas of the lake probably play a more important role in recruitment of benthic Microcystis than deep areas.