Harmful blooms of cyanobacteria (CyanoHABs) have increased globally and cyanotoxins associated with some CyanoHAB species pose serious health risks for animals and humans. CyanoHABs are sensitive to supply rates of both nitrogen and phosphorus, but sensitivity may vary among species (e.g., between diazotrophic and non-diazotrophic species) and a range of physiographic and environmental factors. A sustainable approach to manage CyanoHABs is therefore to limit the supply of nitrogen and phosphorus from catchments to receiving waters. Alternative approaches of within-lake treatment have increased risks and large capital and operational expenditure. The need to manage catchment nutrient loads will intensify with climate change, due to expected increases in nutrient remineralization rates, alteration in hydrological regimes, and increases in lake water temperature and density stratification. Many CyanoHAB species have physiological features that enable them to benefit from the effects of climate change, including positive buoyancy or buoyancy control, high replication rates at elevated water temperature, and nutrient uptake strategies adapted for the intermittency of nutrient supply with greater hydrological variability expected in the future. Greater attention needs to be focused on nonpoint sources of nutrients, including source control, particularly maintaining nitrogen and phosphorus in agricultural soils at or below agronomic optimum levels, and enhancing natural attenuation processes in water and solute transport pathways. Efforts to achieve effective catchment management and avert the dire ecological, human health and economic consequences of CyanoHABs must be intensified in an era of anthropogenically driven environmental change arising from increasing human population, climate change and agricultural intensification.