Low flow rates and persistent thermal stratification can be key factors promoting cyanobacterial blooms. Australia’s
largest river, the iconic Murray River, is highly regulated through a series of weirs and dams. In these riverine weir pools, flow is reduced, and conditions may more closely resemble those of lentic systems where persistent thermal stratification is more common. Potentially toxic cyanobacterial blooms are occurring at an increasing rate in the Murray River, however, the role of river flow rates and thermal stratification is not well understood. To test this, we measured hydrodynamics, climatic conditions, and vertical temperature profiles in weir pools of the Murray River and linked these data to cyanobacterial abundances. Site-specific threshold flow rates for the establishment of persistent stratification were determined, for example, discharges of <4000 ML day at the Kulnine weir pool and ambient maximal air temperatures >30°C. The data collected was used to model thermal stratification over the past two decades for comparison to historical algal data over this period. The analysis of historical algal data showed a positive correlation between increased thermal stratification and reduced flow and certain cyanobacterial genera including Aphanizomenon and Dolichospermum. However, many other bloom-forming cyanobacteria were not strongly related to flow, and other factors may be important for their growth. These results may be useful in informing flow management to reduce the environmental and economic costs of some blooms.