SUMMARY 1. From measurements at several weir pool sites along the turbid and freshwater Barwon‐Darling River, Australia, the development of persistent stratification (for periods of >5 days) was related to river discharge. For the sites examined, the required discharge to allow the development of persistent stratification was between 100 and 450 ML day−1 during the hotter months. High discharge during the hotter months did not allow the formation of persistent stratification, although diel stratification did occur. Low discharge through the cooler months resulted in diel stratification, although persistent stratification lasting for a few days could occur at times. 2. The growth and dominance of Anabaena circinalis at these sites was closely related to the establishment and maintenance of persistent and strong thermal stratification. Growth only occurred during extended periods (>5 days) of persistent stratification. These conditions not only restrict the displacement of A. circinalis downstream, they also allowed the alga to accumulate in surface waters. 3. The discharge levels required to suppress the formation of persistent stratification at the study sites were variable because of large differences in channel cross‐sectional area. To compensate for this variation, the discharges were converted to flow velocities. A critical velocity of 0.05 ms−1 was sufficient for the suppression of persistent thermal stratification and concurrent A. circinalis growth for all sites. The turbulent velocity (u*) under weak wind mixing at the study locations varied between 2.66 × 10−3 and 2.91 × 10−3 ms−1 at the critical flow velocities. These values may have potential to be applied to other rivers in similar climatic zones to suppress nuisance cyanobacterial growth.