To prevent flooding of the Dutch delta, former estuaries have been impounded by the building of dams and sluices. Some of these water bodies, however, experience major ecological problems. One of the problem areas is the former Volkerak estuary that was turned into a freshwater lake in 1987. From the early 1990s onward, toxic Microcystis blooms dominate the phytoplankton of the lake every summer. Two management strategies have been suggested to suppress these harmful algal blooms: flushing the lake with fresh water or reintroducing saline water into the lake. This study aims at an advance assessment of these strategies through the development of a mechanistic model of the population dynamics of Microcystis. To calibrate the model, we monitored the benthic and pelagic Microcystis populations in the lake during two years. Field samples of Microcystis were incubated in the laboratory to estimate growth and mortality rates as functions of light, temperature, and salinity. Recruitment and sedimentation rates were measured in the lake, using traps, to quantify benthic–pelagic coupling of the Microcystis populations. The model predicts that flushing with fresh water will suppress Microcystis blooms when the current flushing rate is sufficiently increased. Furthermore, the inlet of saline water will suppress Microcystis blooms for salinities exceeding 14 g/L. Both management options are technically feasible. Our study illustrates that quantitative ecological knowledge can be a helpful tool guiding large‐scale water management.