Abstract: As one of the in-situ algal control technologies for lakes and reservoirs, water lifting aeration (WLA) technology has controlled algae by promoting water body mixing and enhancing dissolved oxygen in numerous water sources in China. To investigate the effect of WLA technology on cyanobacterial blooms control under different operating conditions in southern reservoirs, a tracking investigation was conducted from June to July 2022 on a southern Chinese reservoir with operating WLA, adjusting them to different operating conditions and setting up two sampling points in the old and new reservoir areas for monitoring. Comparisons of environmental factors such as water temperature, mixing state, nutrient concentration, and algal density between the direct control action area (X1) and the non-direct control action area (X2) before and after system operation revealed significant differences. Principal coordinate analysis (PCoA) was applied to explore the differences in dominant cyanobacteria species before and after the operation of the system, while redundancy analysis and Pearson's correlation analysis were conducted to examine the relationship between these species and environmental factors. The results showed that water temperature, relative water column stability (RWCS) and total phosphorus (TP) were important environmental factors affecting the structure of cyanobacterial communities. WLA effectively controlled the cyanobacterial bloom by lowering the surface water temperature to 28 °C, RWCS index to below 200, and reducing TP concentration by 61.42%. Intermittent operation only temporarily reduced algal density by 39.33% at high temperatures, whereas continuous operation significantly improved the algal control efficiency by reducing algal density by 79.11%. Although significant precipitation events reduced the thermal stability of the water in the short term, the effect of natural mixing was similar in continuous operation and in heavy rainfall conditions, which reduced surface algal density by 71.73%. The results of the study provided practical guidance for reservoir management. It was recommended to achieve algae control by extending the operating time of the system under hot summer weather, and to suspend the operation to save energy under heavy rainfall.