Aeration and mixing have been proven as effective in situ water quality improvement methods, particularly for deep drinking water reservoirs. While there is some research on the mechanism of water quality improvement during artificial mixing, the changes to water quality and the microbial community during the subsequent continuous mixing process is little understood. In this study, we investigate the mechanism of water quality improvement during the continuous mixing process in a drinking water reservoir. During this period, we found a reduction in total nitrogen (TN), total phosphorus (TP), ammonium-nitrogen (NH4-N), iron (Fe), manganese (Mn), and total organic carbon (TOC) of 12.5%–30.8%. We also measured reductions of 8.6% and 6.2% in TN and organic carbon (OC), respectively, in surface sediment. Microbial metabolic activity, abundance, and carbon source utilization were also improved. Redundancy analysis indicated that temperature and dissolved oxygen (DO) were key factors affecting changes in the microbial community. With intervention, the water temperature during continuous mixing was 15 °C, and the mixing temperature in the reservoir increased by 5 °C compared with natural mixing. Our research shows that integrating and optimizing the artificial and continuous mixing processes influences energy savings. This research provides a theoretical basis for further advancing treatment optimizations for a drinking water supply.