Changes in the buoyancy of Microcystis populations were followed over 24 h periods in two shallow well-mixed lakes, Lake Vinkeveen (area 0.6 km2) and Lake IJsselmeer (1190 km-2), in the Netherlands. The Microcystis colonies collected from the surface layers in both lakes showed a buoyancy decrease during the day and an increase at night. The buoyant colonies, and especially the faster-moving large ones, became concentrated by flotation into the surface mixed layers. As a result the mean position of the cyanobacterial population became located nearer the surface than that of other non-buoyant phytoplankton, such as Scenedesmus. The cyanobacteria would, therefore, have received a higher average irradiance. The Microcystis in these shallow lakes had weaker gas vesicles than those found previously in deeper lakes but it was demonstrated that the loss of buoyancy, which occurred at high irradiances, resulted from an increase in carbohydrate ballast rather than through turgor-driven gas vesicle collapse.