Ecosystem activation system (EAS) was developed to create beneficial conditions for microbiome recovery and then restore and maintain the ecological integrity (microbial community, phytoplankton, zooplankton) for eutrophic freshwater rehabilitation. A 30 day's filed test of EAS indicated that over 50% of contaminant was removed and the algae visibly disappeared. EAS treatment 2.5-fold increased the diversity of microbial community and changed the microbial community structure (e.g., two and three-fold decrease in the amount of Flavobacterium and Pseudomonas, typical abundant species of eutrophic freshwater, respectively). Further, the diversity of phytoplankton and zooplankton of treated water suggested that these species were diverse. Representative phytoplankton of eutrophic freshwater, Chlorella and Chlamydomonas were undetectable. The possible mechanism of EAS is restoring the trophic levels of the water body via bottom-up approach by microbial community.