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There are three requirements for phytoplankton growth; a nutrient source, an adequate light supply and an inoculum from which the population can propagate. The cyanobacteria are well adapted to scavenge for these resources in stratified waterbodies. In the lower River Murray, Australia, low flow conditions can lead to stratification and a suitable habitat for cyanobacteria. During these periods Anabaena spp. tend to grow, whereas during high flow there is no stratification, and the diatom Aulacoseira dominates. Consequently, in regulated rivers the magnitude and timing of discharge can be manipulated to disrupt stratification every few days, thereby controlling cyanobacterial growth. Similarly, in reservoirs the cyanobacteria tend to dominate when the water-column is stratified. At Myponga Reservoir Anabaena populations grew when the surface mixed layer became shallow and the cells remained entrained near the surface. Artificial destratification is one of few available management options available to control cyanobacteria. However, techniques are still required to effectively disrupt the surface mixed layer which escapes entrainment by conventional bubble plume aerators. The internal nutrient load can also be controlled with artificial destratification, which along with catchment sources of nutrients, contribute to the magnitude of the phytoplankton biomass. Includes 42 references, table, figures.