The invention discloses an in-situ treatment method for improving the quality of a water environment. The in-situ treatment method is used for treating a river channel water body and comprises the following steps: firstly, laying an aeration system and aquatic plant-imitated filler; secondly, debugging and training a microbial system; thirdly, continuously operating the microbial system until a governed river channel water body reaches V type water body; fourthly, constructing a water ecosystem; fifthly, continuously operating the water ecosystem until the governed river channel water body reaches IV type water body. According to the method, a water body is treated and purified by adopting an in-situ treatment mode, and land is not occupied; energy consumption is equivalent to or lower than that of a water treatment facility of source controlling and sewage intercepting construction; the bottom of the water body is aerated, and bottom mud is consumed in situ, so that the improvement on bottom sediment is facilitated, and desilting investment is greatly reduced or desilting is avoided; microbial communities are enriched by natural aeration, and the treatment effect of water quality is good; the water ecosystem is constructed to sufficiently realize the self-cleaning capability of the water body and prevent and control eutrophication of the water body; the in-situ treatment method is automatically operated and convenient to manage, and can realize unattended operation.