1. In eutrophic lakes, large amounts of the cyanobacterium Microcystis may overwinter in the sediment and re-inoculate the water column in spring. 2. We monitored changes in pelagic and benthic populations of Microcystis in Lake Volkerak, The Netherlands. In addition, sedimentation rates and the rate of recruitment from the sediment were measured using traps. These data were used to model the coupling between the benthic and pelagic populations and to calculate the contribution of overwintering benthic and pelagic populations to the magnitude of the pelagic summer bloom. 3. Changes in the benthic Microcystis population showed a time lag of 3-14 weeks compared with the pelagic population. This time lag increased with lake depth. The largest amount of benthic Microcystis was found in the deepest parts of the lake. These observations suggest horizontal transport of sedimented Microcystis from shallow to deep parts of the lake. 4. Recruitment from and sedimentation to the sediment occurred throughout the year, with highest recruitment and sedimentation rates during summer. Model simulations indicate that the absence of benthic recruitment would reduce the summer bloom by 50%. 5. In spring, the total pelagic population was three to six times smaller than the total benthic population. Yet, model simulations predict that the absence of this small overwintering pelagic population would reduce the summer bloom by more than 64%. 6. Reduction of the overwintering pelagic populations, for instance by flushing, may be a useful management strategy to suppress or at least delay summer blooms of Microcystis.