Eco-engineering is an important tool for wetland restoration, but there are still large theoretical and application gaps in the knowledge of the effects of eco-engineering implementation on the interactions between environmental conditions and organisms during wetland restoration processes. In this study, we investigated water quality parameters and plankton communities in a national wetland park to clarify the mechanism of changes in plankton community structure and their ecological networks before and after the eco-engineering project. Undoubtedly, we found water quality was significantly improved with increased metazooplankton diversity after the implementation of eco-engineering. Ecological engineering reduced the effect of farmland drainage on the restored wetland and changed the phytoplankton community structure, which significantly reduced the relative abundance of Cyanobacteria and increased the relative abundance of Bacillariophyta. The structural equation modeling revealed that the total effect of metazooplankton on phytoplankton was significantly enhanced and associated with weakened relationships between phytoplankton and environmental variables after eco-engineering. In addition, the ecological network analysis also showed that the network connection between phytoplankton and metazooplankton was stronger after the eco-engineering implementation, leading to an enhanced biotic interactions in different trophic levels. These results indicate that the main approach to regulating primary producers in wetland ecosystems changed from “bottom-up” control to a combination of “bottom-up” and “top-down” control under the intervention of artificial recovery measures. Our findings shed new light on the effects of eco-engineering on the interactions between water quality and organisms and provide a scientific basis for the sustainable management of wetland ecosystems.

Eco-Engineering Improves Water Quality and Mediates Plankton–Nutrient Interactions in a Restored Wetland