Supersaturated dissolved oxygen and magnetization (SDOXM) technology is a composite technology that combines supersaturated dissolved oxygen with water magnetization technologies. Compared with conventional water purification technology, the advantages introduced by such technology include obvious and efficient improvement in purified water quality without adding any chemicals, removing sludge and changing the original function of the river. In this study, taking the Middle-Route (MR) of the South-to-North Water Diversion Project of China (SNWDPC) as a pilot project, the effects of the SDOXM composite process on microbial activity, phytoplankton community structure, and removal efficiency of the main nutritional indexes in the canal of the MR were evaluated. Aiming at static and flowing water bodies, this study was divided into two parts: static and dynamic experiments (two groups: a group with artificial aquatic plants and another group without artificial aquatic plants). The performance of the SDOXM system was assessed by monitoring the organic matter removal as well as the relative light unit (RLU) of ATP, changes in the community structure of phytoplankton, and the effects of artificial aquatic plants as a biofilm carrier on organic matter removal and microbial activity. During the study period, SDOXM technology was able to increase the concentration of dissolved oxygen (DO) in water and maintained the state of supersaturation for more than three days. The removal effect of organic matter from water was obvious. The community structure of phytoplankton changed from the Bacillariophyta-Cyanophyta type to the Bacillariophyta-Cyanobacteria type. Finally, the introduction of artificial aquatic plants has contributed to the improvement in water quality. Therefore, SDOXM technology can be used as a new water quality improvement technology to enhance the self-restoration ability of a river natural ecology.