Blue-green algae (or cyanobacteria) form regularly massive blooms in the Baltic Sea – especially in late summer. The bacteria can produce toxins and add bioavailable nitrogen fixed from the atmosphere to the already over-fertilized system. In the presented study, high-resolution model data from the Baltic Sea were combined with various observations. Simulated currents were used to trace the origin of blooms and to analyze water properties during bloom formation. The results of the study are surprising in that the blooms develop in the open Baltic Sea instead of, as might be expected, near the coast. This indicates that complex interactions between the different phytoplankton species may be at play and that hypotheses about simple direct relationships to the nutrient composition of the seawater should be considered with some caution.