Artificial destratification is a promising strategy for managing in-reservoir water quality and mitigating downstream impacts, including cold water pollution. The initial commissioning of an artificial destratification system is a significant disturbance to the reservoir phytoplankton community and results in sudden changes in water column stability, temperature and nutrient distribution. The effects of these changes on the phytoplankton community, in particular cyanobacteria, need to be understood. This study reports on the short-term response of the cyanobacterial community in Pindari Dam, NSW, Australia to a 6-week trial of a bubble plume destratification system between February and March 2026. Before the trial, a co-dominant bloom consisting of Anabaenopsis elenkinii (A. elenkinii) and Dolichospermum planctonicum (D. planctonicum) began to form (total cyanobacterial surface biovolume of 2.6 mm3/L). The operation of the bubble plume unit rapidly decreased the thermocline depth from between 6-7 m to between 2-3 m and redistributed nutrients and trace metals from the hypolimnion into surface waters. Total cyanobacterial biovolume, dominated by D. planctonicum, peaked two weeks into the trial, with surface biovolumes above recreational water guidelines (red level alert, >10 mm3/L). Following this, Dolichospermum perturbatum dominated in the cooler surface water temperatures and sustained higher nutrient availability, with surface biovolumes up to 5 mm3/L. Following the end of the destratification trial, the thermocline depth deepened, and Dolichospermum circinale (D. circinale) became the dominant cyanobacterium in the reservoir. This study highlights the dynamic changes that can occur at the species level in response to changes in environmental conditions and suggests timing the operation of destratification systems to maximise mixing and the suppression of cyanobacterial dominance.