In summer 1997-1998, a bloom of the cyanobacteria Anabaena circinalis (Rabenhorst) and Anabaena spiroides (Klebahn) contaminated the Canning River (Perth, WA), forcing its closure to the public for swimming and fishing. We investigated the major nutrient fluctuations before, during and after the bloom. The river was persistently temperature stratified at least 1 month prior to the bloom. The surface and bottom layers of water had distinctly different nutrient concentrations, which meant that biomass and growth rates of the phytoplankton within each layer were limited by different nutrients. At the peak of the bloom, in the bottom waters growth rates were light limited and biomass was nitrogen limited, whereas in the surface waters biomass was controlled by phosphorus (P) availability and growth rates were probably limited by the lack of dissolved inorganic carbon. Another consequence of stratification was that, at the peak of the bloom (0.25 mg chlorophyll L-1), the mostly buoyant cyanobacteria could not access 83% of the P released from sediments during the summer period of anoxia. In this situation, the injection of oxygenated water, tested as a remediation measure for algal blooms, is likely to exacerbate a bloom by providing more of the limiting nutrient to the surface layer. However, aeration prior to the bloom may reduce P release from the sediments by preventing anoxia.